Modified cell and use thereof in gene and cell therapy

ABSTRACT

The present disclosure describes compositions and methods for treating cancer. Embodiments relate to a cell modified to express one or more molecules at a level that is higher or lower than the level of the one or more molecules expressed by a cell that has not been modified to express the one or more molecules, wherein the one or more molecules comprise Cavin3, ZBED2, and MYC.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application 63/086,343, filed Oct. 1, 2020, which is hereby incorporated by reference in its entirety.

SEQUENCE LISTING INFORMATION

A computer readable textfile, entitled “ST25.txt,” created on or about Sep. 21, 2021, with a file size of about 41.3 KB, contains the sequence listing for this application and is hereby incorporated by reference in its entirety.

TECHNICAL FIELD

The present disclosure relates to compositions and methods for expanding and maintaining modified cells including genetically modified cells, for example, maintaining the number of modified cells, and uses thereof in the treatment of diseases, including cancer.

BACKGROUND

Chimeric antigen receptor (CAR) T cell therapy made significant progress for treating blood cancer such as leukemia, lymphoma, and myeloma. However, the therapy faces many challenges, such as physical barrier, tumor microenvironment immunosuppression, tumor heterogeneity, target specificity, and cell expansion in vivo for the treatment of solid tumors.

SUMMARY

The present disclosure describes compositions and methods for treating cancer. Embodiments relate to a cell modified to express one or more molecules at a level that is higher or lower than the level of the one or more molecules expressed by a cell that has not been modified to express the one or more molecules, wherein the one or more molecules are identified in single-cell profiling analysis. Embodiments relate to a modified cell engineered to express an antigen binding molecule, wherein the expression and/or function of one or more molecules in the modified cell has been enhanced or reduced (including eliminated), where the one or more molecules are identified in single-cell profiling analysis. In embodiments, the modified cell comprises a disruption in an endogenous gene or addition of an exogenous gene that is associated with a biosynthesis or transportation pathway of one or more molecules. In embodiments, the one more molecules comprise at least one of JAK2, STAT1, STAT2, STAT3, STAT4, PRKCA, PRKCQ, MAP3K1, MAP3K4, MAP3K8, MAPK14, BRAF, SMADS, IL2RB, IL12RB2, IL18R1, IL21R, IL7R, CD28, Cavin3, ZBED2, MYC, EGFR, HER2, HER3, HER4, VEGFR2, VEGFR3, PDGFRα, PDGFRβ, gp130, IL-23R, IL-7R, CRLF2, βc, GHR, THPOR, EPOR, LepR, CSF3R, TNFR1, TGFBR1, TGFBR2, ACVR1A, BMPR2 ACVR1B, CXCR1, CXCR2, CXCR3, CXCR4, CCR2, CCRS, TOX, TOX2, TOX4, NR4A2, NR4A3, a functional variant of the one or more molecules, or a functional fragment of the one or more molecules. The one or more molecules can be overexpressed or inducibly overexpressed.

Embodiments relate to a cell modified to express one or more molecules at a level that is higher or lower than the level of the one or more molecules expressed by a cell that has not been modified to express the one or more molecules, wherein the one or more molecules comprise at least one of Cavin3, ZBED2, and MYC

This Summary is not intended to identify key features or essential features of the claimed subject matter, nor is it intended to be used to limit the scope of the claimed subject matter.

BRIEF DESCRIPTION OF THE DRAWINGS

The Detailed Description is described with reference to the accompanying figures. The use of the same reference numbers in different figures indicates similar or identical items.

FIG. 1 shows schematic examples of modified cells.

FIG. 2 shows schematic examples of constructs with respect to the embodiments described in FIG. 1.

FIGS. 3A and 3B show the expression of markers for exhaustion on various cells (P value<0.05=*, <0.01=**, <0.001=***, <0.0001=****; P≥0.05=no significance=NS).

FIGS. 4A, 4B, 5, 6A, and 6B show the proportion of memory T cells, central memory T (Tcm) cells, and stem-like central memory T (Tscm) cells of the various cultured cells of FIG. 3.

FIGS. 7A, 7B, and 7C show activation of B cells that are cultured with various cells.

FIG. 8 shows results of flow cytometry analysis of sorting of B cells and T cells.

FIGS. 9 and 10 show results of flow cytometry analysis of expression of cell markers of co-cultured cells, including B cells and T cells in the presence or absence of CD3-CD19 bispecific antibody

FIG. 11 shows results of flow cytometry analysis of cytokine release by the cells of FIGS. 9 and 10.

FIG. 12 shows results of flow cytometry analysis of PAP CART cells co-cultured with B cells in the presence or absence of CD3-CD19 bispecific antibody. PAP CAR T cells were generated and cultured for 7 days.

FIGS. 13A, 13B, 13C, and 13D show histograms of results of flow cytometry analysis of expression of various markers on T cells and B cells in experiments described in FIG. 92.

FIG. 14 shows CellTrace™ analysis of 6503 cells (i.e., ACPP CART cells) co-cultured with B cells in the presence or absence of CD3-CD19 bispecific antibody.

FIG. 15 shows CellTrace™ analysis of 6503 cells co-cultured with B cells in the presence or absence of CD3-CD19 bispecific antibody.

FIGS. 16A and 16B show CellTrace™ analysis of 6503 cells co-cultured with B cells in the presence or absence of CD3-CD19 bispecific antibody.

FIGS. 17A, 17B, 17C, and 17D show cytokine release results of CAR T cells co-cultured with B cells in the presence or absence of CD3-CD19 bispecific antibody.

FIG. 18 shows gene expression profiling results of single-cell RNA (scRNA) analysis.

FIG. 19 shows gene expression profiling results of scRNA analysis.

FIG. 20 shows B cell clustering 24 hours after CD19 CART cells and PAP CAR T cells were co-cultured with these B cells.

FIG. 21 shows the expression of surface markers of the B cells.

FIG. 22 shows PAP CART cells clustering 24 and 48 hours after CD19 CART cells and PAP CAR T cells were co-cultured with B cells.

FIG. 23 shows highly expressed genes in PAP CAR T cells in TC1.

FIGS. 24A and 24B show that T cells derived from both peripheral blood (PB) and tumor tissue of a colorectal cancer patient with thyroid cancer are capable of robust proliferation and cytotoxicity.

FIG. 25 shows that identification of all T cell clusters in PB and tumor tissue was evidenced by the expression of signature genes and known functional markers.

FIGS. 26A, 26B, and 26C show that TSHR CAR T cells are significantly enriched in tumor tissue, confirming the capacity of CAR T cell infiltration into the tumor. These data are restricted to just TSHR CAR T cells.

FIGS. 27A, 27B, 27C, and 27D show rare clonotype was found to be shared by TSHR CAR T cells in PB and tumor tissue.

FIGS. 28A, 28B, 28C, and 28D show an inferred developmental trajectory of CAR+CD8 T cells in PB, suggesting a branched structure with differentiated proliferation and cytotoxicity of T cells.

FIGS. 29A, 29B, 29C, and 29D show another inferred developmental trajectory of CAR+CD8 T cell in tumor tissue suggesting a branched structure with differentiated proliferation and cytotoxicity of T cells.

FIG. 30 shows TSHR CAR T cells in tumor tissue exhibited a higher degree of trafficking and cytotoxicity, as compared with TSHR CAR T cells from PB.

FIG. 31 shows a schematic diagram of vectors.

FIG. 32 shows results of flow cytometry analysis of T cells expressing CAR, MYD88, and the intracellular domain of CD40.

FIGS. 33A and 33B show a schematic diagram of CAR and a portion of a modified cell, and a schematic diagram of CAR-DC.

FIGS. 34A and 34B show CAR expression and phenotypes of CAR T cells expressing CAVIN3 or ZBED2.

FIG. 35 shows cell activation of CAR T cells expressing CAVIN3 or ZBED2 after co-cultured with substrate cells NALM6.

FIG. 36 shows cell exhaustion of CAR T cells expressing CAVIN3 or ZBED2 after co-cultured with substrate cells NALM6.

FIG. 37 shows cell phenotype changes of CAR T cells expressing CAVIN3 or ZBED2 after co-cultured with substrate cells NALM6.

FIG. 38A, 38B, and 38C show cytokine release of CAR T cells expressing CAVIN3 or ZBED2 after co-cultured with substrate cells NALM6.

FIG. 39 shows tumor inhibition assay results of CAR T cells expressing CAVIN3 or ZBED2 after co-cultured with substrate cells NALM6.

FIG. 40 shows cell expansion of CAR T cells expressing CAVIN3 or ZBED2.

DETAILED DESCRIPTION

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary skill in the art to which the disclosure belongs. Although any method and material similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, preferred methods and materials are described. For the purposes of the present disclosure, the following terms are defined below.

The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.

By “about” is meant a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight, or length that varies by as much as 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length.

The term “activation,” as used herein, refers to the state of a cell that has been sufficiently stimulated to induce detectable cellular proliferation. Activation can also be associated with induced cytokine production and detectable effector functions. The term “activated T cells” refers to, among other things, T cells that are undergoing cell division.

The term “antibody” is used in the broadest sense and refers to monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity or function. The antibodies in the present disclosure may exist in a variety of forms including, for example, polyclonal antibodies; monoclonal antibodies; Fv, Fab, Fab′, and F(ab′)₂ fragments; as well as single chain antibodies and humanized antibodies (Harlow et al., 1999, In: Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY; Harlow et al., 1989, In: Antibodies: A Laboratory Manual, Cold Spring Harbor, New York; Houston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; Bird et al., 1988, Science 242:423-426).

The term “antibody fragments” refers to a portion of a full-length antibody, for example, the antigen binding or variable region of the antibody. Other examples of antibody fragments include Fab, Fab′, F(ab′)₂, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.

The term “Fv” refers to the minimum antibody fragment, which contains a complete antigen-recognition and -binding site. This fragment consists of a dimer of one heavy- and one light-chain variable region domain in a tight, non-covalent association. From the folding of these two domains emanates six hypervariable loops (3 loops each from the H and L chain) that contribute amino acid residues for antigen binding and confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv including only three complementarity determining regions (CDRs) specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site (the dimer).

An “antibody heavy chain,” as used herein, refers to the larger of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations. An “antibody light chain,” as used herein, refers to the smaller of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations. K and A light chains refer to the two major antibody light chain isotypes.

The term “synthetic antibody” refers to an antibody that is generated using recombinant DNA technology, such as, for example, an antibody expressed by a bacteriophage. The term also includes an antibody that has been generated by the synthesis of a DNA molecule encoding the antibody and the expression of the DNA molecule to obtain the antibody or to obtain an amino acid encoding the antibody. Synthetic DNA is obtained using technology that is available and well known in the art.

The term “antigen” refers to a molecule that provokes an immune response, which may involve either antibody production, or the activation of specific immunologically competent cells, or both. Antigens include any macromolecule, including all proteins or peptides or molecules derived from recombinant or genomic DNA. For example, DNA including a nucleotide sequence or a partial nucleotide sequence encoding a protein or peptide that elicits an immune response, and therefore, encodes an “antigen” as the term is used herein. An antigen need not be encoded solely by a full-length nucleotide sequence of a gene. An antigen can be generated, synthesized, or derived from a biological sample including a tissue sample, a tumor sample, a cell, or a biological fluid.

The term “anti-tumor effect,” as used herein, refers to a biological effect associated with a decrease in tumor volume, a decrease in the number of tumor cells, a decrease in the number of metastases, decrease in tumor cell proliferation, decrease in tumor cell survival, an increase in life expectancy of a subject having tumor cells, or amelioration of various physiological symptoms associated with the cancerous condition. An “anti-tumor effect” can also be manifested by the ability of the peptides, polynucleotides, cells, and antibodies in the prevention of the occurrence of tumor in the first place.

The term “auto-antigen” refers to an endogenous antigen mistakenly recognized by the immune system as being foreign. Auto-antigens include cellular proteins, phosphoproteins, cellular surface proteins, cellular lipids, nucleic acids, glycoproteins, including cell surface receptors.

The term “autologous” is used to describe a material derived from a subject that is subsequently re-introduced into the same subject.

The term “allogeneic” is used to describe a graft derived from a different subject of the same species. As an example, a donor subject may be related or unrelated to the recipient subject, but the donor subject has immune system markers which are similar to the recipient subject.

The term “xenogeneic” is used to describe a graft derived from a subject of a different species. As an example, the donor subject is from a different species than a recipient subject, and the donor subject and the recipient subject can be genetically and immunologically incompatible.

The term “cancer” is used to refer to a disease characterized by the rapid and uncontrolled growth of aberrant cells. Cancer cells can spread locally or through the bloodstream and lymphatic system to other parts of the body. Examples of various cancers include breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, renal cancer, liver cancer, brain cancer, lymphoma, leukemia, lung cancer, and the like.

Throughout this specification, unless the context requires otherwise, the words “comprise,” “includes,” and “including” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements.

The phrase “consisting of” is meant to include, and is limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of” indicates that the listed elements are required or mandatory and that no other elements may be present.

The phrase “consisting essentially of” is meant to include any element listed after the phrase and can include other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements. For example, if the element does not affect the expansion, function, or phenotype of the cells, then the element is not required and is considered optional.

The terms “complementary” and “complementarity” refer to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules. For example, the sequence “A-G-T,” is complementary to the sequence “T-C-A.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules, or there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.

The term “corresponds to” or “corresponding to” refers to (a) a polynucleotide having a nucleotide sequence that is substantially identical or complementary to all or a portion of a reference polynucleotide sequence or encoding an amino acid sequence identical to an amino acid sequence in a peptide or protein, or (b) a peptide or polypeptide having an amino acid sequence that is substantially identical to a sequence of amino acids in a reference peptide or protein.

The term “co-stimulatory ligand” refers to a molecule on an antigen-presenting cell (e.g., an APC, dendritic cell, B cell, and the like) that specifically binds a cognate co-stimulatory molecule on a T cell, thereby providing a signal which, in addition to the primary signal provided by, for instance, binding of a TCR/CD3 complex with an MHC molecule loaded with peptide, mediates a T cell response, including at least one of proliferation, activation, differentiation, and other cellular responses. A co-stimulatory ligand can include B7-1 (CD80), B7-2 (CD86), PD-L1, PD-L2, 4-1BBL, OX40L, inducible co-stimulatory ligand (ICOS-L), intercellular adhesion molecule (ICAM), CD30L, CD40, CD70, CD83, HLA-G, MICA, MICB, HVEM, lymphotoxin beta receptor, 3/TR6, ILT3, ILT4, HVEM, a ligand for CD7, an agonist or antibody that binds the Toll ligand receptor, and a ligand that specifically binds with B7-H3. A co-stimulatory ligand also includes, inter alia, an agonist or an antibody that specifically binds with a co-stimulatory molecule present on a T cell, such as CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and a ligand that specifically binds CD83.

The term “co-stimulatory molecule” refers to the cognate binding partner on a T cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the T cell, such as proliferation. Co-stimulatory molecules include an MHC class I molecule, BTLA, and a Toll-like receptor.

The term “co-stimulatory signal” refers to a signal, which in combination with a primary signal, such as TCR/CD3 ligation, leads to T cell proliferation and/or upregulation or downregulation of key molecules.

The terms “disease” and “condition” may be used interchangeably or may be different in that the particular malady or condition may not have a known causative agent (so that etiology has not yet been worked out), and it is therefore not yet recognized as a disease but only as an undesirable condition or syndrome, wherein a more or less specific set of symptoms have been identified by clinicians. The term “disease” is a state of health of a subject wherein the subject cannot maintain homeostasis, and wherein if the disease is not ameliorated, then the subject's health continues to deteriorate. In contrast, a “disorder” in a subject is a state of health in which the animal is able to maintain homeostasis, but in which the animal's state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal's state of health.

The term “effective” refers to adequate to accomplish a desired, expected, or intended result. For example, an “effective amount” in the context of treatment may be an amount of a compound sufficient to produce a therapeutic or prophylactic benefit.

The term “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as a template for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence (except that a “T” is replaced by a “U”) and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.

The term “exogenous” refers to a molecule that does not naturally occur in a wild-type cell or organism but is typically introduced into the cell by molecular biological techniques. Examples of exogenous polynucleotides include vectors, plasmids, and/or man-made nucleic acid constructs encoding the desired protein. With regard to polynucleotides and proteins, the term “endogenous” or “native” refers to naturally occurring polynucleotide or amino acid sequences that may be found in a given wild-type cell or organism. Also, a particular polynucleotide sequence that is isolated from a first organism and transferred to a second organism by molecular biological techniques is typically considered an “exogenous” polynucleotide or amino acid sequence with respect to the second organism. In specific embodiments, polynucleotide sequences can be “introduced” by molecular biological techniques into a microorganism that already contains such a polynucleotide sequence, for instance, to create one or more additional copies of an otherwise naturally-occurring polynucleotide sequence, and thereby facilitate overexpression of the encoded polypeptide.

The term “expression or overexpression” refers to the transcription and/or translation of a particular nucleotide sequence into a precursor or mature protein, for example, driven by its promoter. “Overexpression” refers to the production of a gene product in transgenic organisms or cells that exceeds levels of production in normal or non-transformed organisms or cells. As defined herein, the term “expression” refers to expression or overexpression.

The term “expression vector” refers to a vector including a recombinant polynucleotide including expression control (regulatory) sequences operably linked to a nucleotide sequence to be expressed. An expression vector includes sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes), and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.

Viruses can be used to deliver nucleic acids into a cell in vitro and in vivo (in a subject). Examples of viruses useful for delivery of nucleic acids into cells include retrovirus, adenovirus, herpes simplex virus, vaccinia virus, and adeno-associated virus.

There also exist non-viral methods for delivering nucleic acids into a cell, for example, electroporation, gene gun, sonoporation, magnetofection, and the use of oligonucleotides, lipoplexes, dendrimers, and inorganic nanoparticles.

The term “homologous” refers to sequence similarity or sequence identity between two polypeptides or between two polynucleotides when a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position. The percent of homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared x100. For example, if 6 of 10 of the positions in two sequences are matched or homologous, then the two sequences are 60% homologous. By way of example, the DNA sequences ATTGCC and TATGGC share 50% homology. A comparison is made when two sequences are aligned to give maximum homology.

The term “immunoglobulin” or “Ig,” refers to a class of proteins, which function as antibodies. The five members included in this class of proteins are IgA, IgG, IgM, IgD, and IgE. IgA is the primary antibody that is present in body secretions, such as saliva, tears, breast milk, gastrointestinal secretions, and mucus secretions of the respiratory and genitourinary tracts. IgG is the most common circulating antibody. IgM is the main immunoglobulin produced in the primary immune response in most subjects. It is the most efficient immunoglobulin in agglutination, complement fixation, and other antibody responses and is important in defense against bacteria and viruses. IgD is the immunoglobulin that has no known antibody function but may serve as an antigen receptor. IgE is the immunoglobulin that mediates immediate hypersensitivity by causing the release of mediators from mast cells and basophils upon exposure to the allergen.

The term “isolated” refers to a material that is substantially or essentially free from components that normally accompany it in its native state. The material can be a cell or a macromolecule, such as a protein or nucleic acid. For example, an “isolated polynucleotide,” as used herein, refers to a polynucleotide, which has been purified from the sequences which flank it in a naturally-occurring state, e.g., a DNA fragment that has been removed from the sequences that are normally adjacent to the fragment. Alternatively, an “isolated peptide” or an “isolated polypeptide” and the like, as used herein, refer to in vitro isolation and/or purification of a peptide or polypeptide molecule from its natural cellular environment and from association with other components of the cell.

The term “substantially purified” refers to a material that is substantially free from components that are normally associated with it in its native state. For example, a substantially purified cell refers to a cell that has been separated from other cell types with which it is normally associated in its naturally occurring or native state. In some instances, a population of substantially purified cells refers to a homogenous population of cells. In other instances, this term refers simply to a cell that has been separated from the cells with which they are naturally associated in their natural state. In embodiments, the cells are cultured in vitro. In embodiments, the cells are not cultured in vitro.

In the context of the present disclosure, the following abbreviations for the commonly occurring nucleic acid bases are used. “A” refers to adenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refers to thymidine, and “U” refers to uridine.

Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some versions contain an intron(s).

The term “lentivirus” refers to a genus of the Retroviridae family. Lentiviruses are unique among the retroviruses in being able to infect non-dividing cells; they can deliver a significant amount of genetic information into the DNA of the host cell, so they are one of the most efficient methods of a gene delivery vector. Moreover, the use of lentiviruses enables the integration of genetic information into the host chromosome, resulting in stably transduced genetic information. HIV, SIV, and FIV are all examples of lentiviruses. Vectors derived from lentiviruses offer the means to achieve significant levels of gene transfer in vivo.

The term “modulating” refers to mediating a detectable increase or decrease in the level of a response in a subject compared with the level of a response in the subject in the absence of a treatment or compound and/or compared with the level of a response in an otherwise identical but untreated subject. The term encompasses perturbing and/or affecting a native signal or response, thereby mediating a beneficial therapeutic response in a subject, preferably a human.

Nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence, or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.

The term “under transcriptional control” refers to a promoter being operably linked to and in the correct location and orientation in relation to a polynucleotide to control (regulate) the initiation of transcription by RNA polymerase and expression of the polynucleotide.

The term “overexpressed” tumor antigen or “overexpression” of the tumor antigen is intended to indicate an abnormal level of expression of the tumor antigen in a cell from a disease area such as a solid tumor within a specific tissue or organ of the patient relative to the level of expression in a normal cell from that tissue or organ. Patients having a solid tumor or a hematological malignancy characterized by overexpression of the tumor antigen can be determined by standard assays known in the art.

Solid tumors are abnormal masses of tissue that usually do not contain cysts or liquid areas. Solid tumors can be benign or malignant. Different types of solid tumors are named for the type of cells that form them (such as sarcomas, carcinomas, and lymphomas). Examples of solid tumors, such as sarcomas and carcinomas, include fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, lymphoid malignancy, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer, hepatocellular carcinoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, medullary thyroid carcinoma, papillary thyroid carcinoma, pheochromocytomas sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, Wilms' tumor, cervical cancer, testicular tumor, seminoma, bladder carcinoma, melanoma, and CNS tumors (such as a glioma (such as brainstem glioma and mixed gliomas), glioblastoma (also known as glioblastoma multiforme), astrocytoma, CNS lymphoma, germinoma, medulloblastoma, Schwannoma craniopharyogioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, neuroblastoma, retinoblastoma, and brain metastases).

A solid tumor antigen is an antigen expressed on a solid tumor. In embodiments, solid tumor antigens are also expressed at low levels on healthy tissue. Examples of solid tumor antigens and their related disease tumors are provided in Table 1.

TABLE 1 Solid Tumor antigen Disease tumor PRLR Breast Cancer CLCA1 colorectal Cancer MUC12 colorectal Cancer GUCY2C colorectal Cancer and other digestive cancer types GPR35 colorectal Cancer CR1L Gastric Cancer MUC 17 Gastric Cancer TMPRSS11B esophageal Cancer MUC21 esophageal Cancer TMPRSS11E esophageal Cancer CD207 bladder Cancer SLC30A8 pancreatic Cancer CFC1 pancreatic Cancer SLC12A3 Cervical Cancer SSTR1 Cervical tumor GPR27 Ovary tumor FZD10 Ovary tumor TSHR Thyroid Tumor SIGLEC15 Urothelial cancer SLC6A3 Renal cancer KISS1R Renal cancer QRFPR Renal cancer: GPR119 Pancreatic cancer CLDN6 Endometrial cancer/Urothelial cancer UPK2 Urothelial cancer (including bladder cancer) ADAM12 Breast cancer, pancreatic cancer, and the like SLC45A3 Prostate cancer ACPP Prostate cancer MUC21 Esophageal cancer MUC16 Ovarian cancer MS4A12 Colorectal cancer ALPP Endometrial cancer CEA Colorectal carcinoma EphA2 Glioma FAP Mesotelioma GPC3 Lung squamous cell carcinoma IL13-Rα2 Glioma Mesothelin Metastatic cancer PSMA Prostate cancer ROR1 Breast lung carcinoma VEGFR-II Metastatic cancer GD2 Neuroblastoma FR-α Ovarian carcinoma ErbB2 Carcinomas EpCAM Carcinomas EGFRvIII Glioma-Glioblastoma EGFR Glioma-NSCL cancer tMUC1 Cholangiocarcinoma, Pancreatic cancer, Breast PSCA pancreas, stomach, or prostate cancer FCER2, GPR18, FCRLA, breast cancer CXCR5, FCRL3, FCRL2, HTR3A, and CLEC17A TRPMI, SLC45A2, and Lymphoma SLC24A5 DPEP3 Melanoma KCNK16 ovarian, testis LIM2 or KCNV2 Pancreatic SLC26A4 thyroid cancer CD171 Neuroblastoma Glypican-3 Sarcoma IL-13 Glioma CD79a/b Lymphoma MAGE A4 Lung cancer and multiple cancer types

The term “parenteral administration” of a composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.), intrasternal injection, or infusion techniques.

The terms “patient,” “subject,” and “individual,” and the like are used interchangeably herein and refer to any human or animal, amenable to the methods described herein. In certain non-limiting embodiments, the patient, subject, or individual is a human or animal. In embodiments, the term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals). Examples of subjects include humans, and animals, such as dogs, cats, mice, rats, and transgenic species thereof.

A subject in need of treatment or in need thereof includes a subject having a disease, condition, or disorder that needs to be treated. A subject in need thereof also includes a subject that needs treatment for the prevention of a disease, condition, or disorder.

The term “polynucleotide” or “nucleic acid” refers to mRNA, RNA, cRNA, rRNA, cDNA, or DNA. The term typically refers to a polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxynucleotides, or a modified form of either type of nucleotide. The term includes all forms of nucleic acids, including single and double-stranded forms of nucleic acids.

The terms “polynucleotide variant” and “variant,” and the like refer to polynucleotides displaying substantial sequence identity with a reference polynucleotide sequence or polynucleotides that hybridize with a reference sequence under stringent conditions that are defined hereinafter. These terms also encompass polynucleotides that are distinguished from a reference polynucleotide by the addition, deletion, or substitution of at least one nucleotide. Accordingly, the terms “polynucleotide variant” and “variant” include polynucleotides in which one or more nucleotides have been added or deleted, or replaced with different nucleotides. In this regard, it is well understood in the art that certain alterations inclusive of mutations, additions, deletions, and substitutions can be made to a reference polynucleotide whereby the altered polynucleotide retains the biological function or activity of the reference polynucleotide or has increased activity in relation to the reference polynucleotide (i.e., optimized). Polynucleotide variants include, for example, polynucleotides having at least 50% (and at least 51% to at least 99% and all integer percentages in between, e.g., 90%, 95%, or 98%) sequence identity with a reference polynucleotide sequence described herein. The terms “polynucleotide variant” and “variant” also include naturally-occurring allelic variants and orthologs.

The terms “polypeptide,” “polypeptide fragment,” “peptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues and to variants and synthetic analogues of the same. Thus, these terms apply to amino acid polymers in which one or more amino acid residues are synthetic non-naturally occurring amino acids, such as a chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally-occurring amino acid polymers. In certain aspects, polypeptides may include enzymatic polypeptides, or “enzymes,” which typically catalyze (i.e., increase the rate of) various chemical reactions.

The term “polypeptide variant” refers to polypeptides that are distinguished from a reference polypeptide sequence by the addition, deletion, or substitution of at least one amino acid residue. In embodiments, a polypeptide variant is distinguished from a reference polypeptide by one or more substitutions, which may be conservative or non-conservative. In embodiments, the polypeptide variant comprises conservative substitutions, and, in this regard, it is well understood in the art that some amino acids may be changed to others with broadly similar properties without changing the nature of the activity of the polypeptide. Polypeptide variants also encompass polypeptides in which one or more amino acids have been added or deleted, or replaced with different amino acid residues.

The term “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell or introduced synthetic machinery required to initiate the specific transcription of a polynucleotide sequence. The term “expression control (regulatory) sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.

The term “bind,” “binds,” or “interacts with” refers to a molecule recognizing and adhering to a second molecule in a sample or organism but does not substantially recognize or adhere to other structurally unrelated molecules in the sample. The term “specifically binds,” as used herein with respect to an antibody, refers to an antibody that recognizes a specific antigen but does not substantially recognize or bind other molecules in a sample. For example, an antibody that specifically binds an antigen from one species may also bind that antigen from one or more species. But, such cross-species reactivity does not itself alter the classification of an antibody as specific. In another example, an antibody that specifically binds an antigen may also bind different allelic forms of the antigen. However, such cross reactivity does not itself alter the classification of an antibody as specific. In some instances, the terms “specific binding” or “specifically binding” can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody recognizes and binds a specific protein structure rather than to any protein. If an antibody is specific for epitope “A,” the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled “A” and the antibody, will reduce the amount of labeled A bound to the antibody.

By “statistically significant,” it is meant that the result was unlikely to have occurred by chance. Statistical significance can be determined by any method known in art. Commonly used measures of significance include the p-value, which is the frequency or probability with which the observed event would occur if the null hypothesis were true. If the obtained p-value is smaller than the significance level, then the null hypothesis is rejected. In simple cases, the significance level is defined at a p-value of 0.05 or less. A “decreased” or “reduced” or “lesser” amount is typically a “statistically significant” or a physiologically significant amount and may include a decrease that is about 1.1, 1.2, 1.3, 1.4, 1.5, 1.6 1.7, 1.8, 1.9, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 or more times (e.g., 100, 500, 1000 times) (including all integers and decimal points in between and above 1, e.g., 1.5, 1.6, 1.7. 1.8, etc.) an amount or level described herein.

The term “stimulation” refers to a primary response induced by binding of a stimulatory molecule (e.g., a TCR/CD3 complex) with its cognate ligand, thereby mediating a signal transduction event, such as signal transduction via the TCR/CD3 complex. Stimulation can mediate altered expression of certain molecules, such as downregulation of TGF-β and/or reorganization of cytoskeletal structures.

The term “stimulatory molecule” refers to a molecule on a T cell that specifically binds a cognate stimulatory ligand present on an antigen presenting cell. For example, a functional signaling domain derived from a stimulatory molecule is the zeta chain associated with the T cell receptor complex. The stimulatory molecule includes a domain responsible for signal transduction.

The term “stimulatory ligand” refers to a ligand that when present on an antigen-presenting cell (e.g., an APC, a dendritic cell, a B-cell, and the like.) can specifically bind with a cognate binding partner (referred to herein as a “stimulatory molecule”) on a cell, for example, a T cell, thereby mediating a primary response by the T cell, including activation, initiation of an immune response, proliferation, and similar processes. Stimulatory ligands are well-known in the art and encompass, inter alia, an MHC Class I molecule loaded with a peptide, an anti-CD3 antibody, a superagonist anti-CD28 antibody, and a superagonist anti-CD2 antibody.

The term “therapeutic” refers to treatment and/or prophylaxis. A therapeutic effect is obtained by suppression, remission, or eradication of a disease state or alleviating the symptoms of a disease state.

The term “therapeutically effective amount” refers to the amount of the subject compound that will elicit the biological or medical response of a tissue, system, or subject that is being sought by the researcher, veterinarian, medical doctor or another clinician. The term “therapeutically effective amount” includes that amount of a compound that, when administered, is sufficient to prevent the development of, or alleviate to some extent, one or more of the signs or symptoms of the disorder or disease being treated. The therapeutically effective amount will vary depending on the compound, the disease, and its severity, and the age, weight, etc., of the subject to be treated.

The term “treat a disease” refers to the reduction of the frequency or severity of at least one sign or symptom of a disease or disorder experienced by a subject.

The term “transfected” or “transformed” or “transduced” refers to a process by which an exogenous nucleic acid is transferred or introduced into the host cell. A “transfected” or “transformed” or “transduced” cell is one that has been transfected, transformed, or transduced with an exogenous nucleic acid. The cell includes the primary subject cell and its progeny.

The term “vector” refers to a polynucleotide that comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” includes an autonomously replicating plasmid or a virus. The term also includes non-plasmid and non-viral compounds which facilitate the transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like. Examples of viral vectors include adenoviral vectors, adeno-associated virus vectors, retroviral vectors, and others. For example, lentiviruses are complex retroviruses, which, in addition to the common retroviral genes gag, pol, and env, contain other genes with regulatory or structural functions. Lentiviral vectors are well known in the art. Some examples of lentivirus include the Human Immunodeficiency Viruses: HIV-1, HIV-2, and the Simian Immunodeficiency Virus: SIV. Lentiviral vectors have been generated by multiply attenuating the HIV virulence genes, for example, the genes env, vif, vpr, vpu, and nef are deleted, making the vector biologically safe.

Ranges: throughout this disclosure, various aspects of the disclosure can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6, etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range.

A “chimeric antigen receptor” (CAR) molecule is a recombinant polypeptide including at least an extracellular domain, a transmembrane domain, and a cytoplasmic domain or intracellular domain. In embodiments, the domains of the CAR are on the same polypeptide chain, for example, a chimeric fusion protein. In embodiments, the domains are on different polypeptide chains, for example, the domains are not contiguous.

The extracellular domain of a CAR molecule includes an antigen binding domain. The antigen binding domain is for expanding and/or maintaining the modified cells, such as a CAR T cell, or for killing a tumor cell, such as a solid tumor. In embodiments, the antigen binding domain for expanding and/or maintaining modified cells binds an antigen, for example, a cell surface molecule or marker, on the surface of a WBC. In embodiments, the WBC is at least one of GMP (granulocyte macrophage precursor), MDP (monocyte-macrophage/dendritic cell precursors), cMoP (common monocyte precursor), basophil, eosinophil, neutrophil, SatM (Segerate-nucleus-containing atypical monocyte), macrophage, monocyte, CDP (common dendritic cell precursor), cDC (conventional DC), pDC (plasmacytoid DC), CLP (common lymphocyte precursor), B cell, ILC (Innate Lymphocyte), NK cell, megakaryocyte, myeloblast, promyelocyte, myelocyte, meta—myelocyte, band cells, lymphoblast, prolymphocyte, monoblast, megakaryoblast, promegakaryocyte, megakaryocyte, platelets, or MSDC (Myeloid-derived suppressor cell). In embodiments, the WBC is a granulocyte, monocyte, and or lymphocyte. In embodiments, the WBC is a lymphocyte, for example, a B cell. In embodiments, the WBC is a B cell. In embodiments, the cell surface molecule of a B cell includes CD19, CD22, CD20, BCMA, CDS, CD7, CD2, CD16, CD56, CD30, CD14, CD68, CD11b, CD18, CD169, CD1c, CD33, CD38, CD138, or CD13. In embodiments, the cell surface molecule of the B cell is CD19, CD20, CD22, or BCMA. In embodiments, the cell surface molecule of the B cell is CD19.

The cells described herein, including modified cells such as CAR cells and modified T cells, can be derived from stem cells. Stem cells may be adult stem cells, embryonic stem cells, more particularly non-human stem cells, cord blood stem cells, progenitor cells, bone marrow stem cells, induced pluripotent stem cells, totipotent stem cells, or hematopoietic stem cells. A modified cell may also be a dendritic cell, an NK-cell, a B-cell, or a T cell selected from the group consisting of inflammatory T-lymphocytes, cytotoxic T-lymphocytes, regulatory T lymphocytes, or helper T-lymphocytes. In embodiments, Modified cells may be derived from the group consisting of CD4+ T lymphocytes and CD8+ T lymphocytes. Prior to expansion and genetic modification of the cells, a source of cells may be obtained from a subject through a variety of non-limiting methods. T cells may be obtained from a number of non-limiting sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors. In embodiments, any number of T cell lines available and known to those skilled in the art may be used. In embodiments, modified cells may be derived from a healthy donor, from a patient diagnosed with cancer, or from a patient diagnosed with an infection. In embodiments, a modified cell is part of a mixed population of cells that present different phenotypic characteristics.

A population of cells refers to a group of two or more cells. The cells of the population could be the same, such that the population is a homogenous population of cells. The cells of the population could be different, such that the population is a mixed population or a heterogeneous population of cells. For example, a mixed population of cells could include modified cells comprising a first CAR and cells comprising a second CAR, wherein the first CAR and the second CAR bind different antigens.

The term “stem cell” refers to any of certain types of cells which have the capacity for self-renewal and the ability to differentiate into other kind(s) of a cell. For example, a stem cell gives rise either to two daughter stem cells (as occurs in vitro with embryonic stem cells in culture) or to one stem cell and a cell that undergoes differentiation (as occurs, e.g., in hematopoietic stem cells, which give rise to blood cells). Different categories of stem cells may be distinguished on the basis of their origin and/or on the extent of their capacity for differentiation into other types of cells. For example, stem cells may include embryonic stem (ES) cells (i.e., pluripotent stem cells), somatic stem cells, induced pluripotent stem cells, and any other types of stem cells.

The pluripotent embryonic stem cells are found in the inner cell mass of a blastocyst and have an innate capacity for differentiation. For example, pluripotent embryonic stem cells have the potential to form any type of cell in the body. When grown in vitro for long periods of time, ES cells maintain pluripotency as progeny cells retain the potential for multilineage differentiation.

Somatic stem cells can include fetal stem cells (from the fetus) and adult stem cells (found in various tissues, such as bone marrow). These cells have been regarded as having a capacity for differentiation that is lower than that of the pluripotent ES cells—with the capacity of fetal stem cells being greater than that of adult stem cells. Somatic stem cells apparently differentiate into only a limited number of types of cells and have been described as multipotent. The “tissue-specific” stem cells normally give rise to only one type of cell. For example, embryonic stem cells may be differentiated into blood stem cells (e.g., hematopoietic stem cells (HSCs)), which may be further differentiated into various blood cells (e.g., red blood cells, platelets, white blood cells, etc.).

Induced pluripotent stem cells (i.e., iPS cells or iPSCs) may include a type of pluripotent stem cell artificially derived from a non-pluripotent cell (e.g., an adult somatic cell) by inducing an expression of specific genes. Induced pluripotent stem cells are similar to natural pluripotent stem cells, such as embryonic stem (ES) cells, in many aspects, such as the expression of certain stem cell genes and proteins, chromatin methylation patterns, doubling time, embryoid body formation, teratoma formation, viable chimera formation, and potency and differentiability. Induced pluripotent cells can be obtained from adult stomach, liver, skin, and blood cells.

In embodiments, the antigen binding domain for killing a tumor binds an antigen on the surface of a tumor, for example, a tumor antigen or tumor marker. Tumor antigens are proteins that are produced by tumor cells that elicit an immune response, particularly T cell mediated immune responses. Tumor antigens are well known in the art and include, for example, tumor associated MUC1 (tMUC1), a glioma-associated antigen, carcinoembryonic antigen (CEA), β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut hsp70-2, M-CSF, prostase, prostate-specific antigen (PSA), PAP, NY-ESO-1, LAGE-1a, p53, prostein, PSMA, Her2/neu, surviving, telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, CD22, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, CD19, and mesothelin. For example, when the tumor antigen is CD19, the CAR thereof can be referred to as CD19 CAR (19CAR, CD19 CAR, or CD19-CAR), which is a CAR molecule that includes an antigen binding domain that binds CD19.

In embodiments, the extracellular antigen binding domain of a CAR includes at least one scFv or at least a single domain antibody. As an example, there can be two scFvs on a CAR. The scFv includes a light chain variable (VL) region and a heavy chain variable (VH) region of a target antigen-specific monoclonal antibody joined by a flexible linker. Single chain variable region fragments can be made by linking light and/or heavy chain variable regions by using a short linking peptide (Bird et al., Science 242:423-426, 1988). An example of a linking peptide is the GS linker having the amino acid sequence (GGGGS)₃ (SEQ ID NO: 30), which bridges approximately 3.5 nm between the carboxy terminus of one variable region and the amino terminus of the other variable region. Linkers of other sequences have been designed and used (Bird et al., 1988, supra). In general, linkers can be short, flexible polypeptides and preferably comprised of about 20 or fewer amino acid residues. The single chain variants can be produced either recombinantly or synthetically. For synthetic production of scFv, an automated synthesizer can be used. For recombinant production of scFv, a suitable plasmid containing a polynucleotide that encodes the scFv can be introduced into a suitable host cell, either eukaryotic, such as yeast, plant, insect, or mammalian cells, or prokaryotic, such as E. coli. Polynucleotides encoding the scFv of interest can be made by routine manipulations such as ligation of polynucleotides. The resultant scFv can be isolated using standard protein purification techniques known in the art.

The cytoplasmic domain of the CAR molecules described herein includes one or more co-stimulatory domains and one or more signaling domains. The co-stimulatory and signaling domains function to transmit the signal and activate molecules, such as T cells, in response to antigen binding. The one or more co-stimulatory domains are derived from stimulatory molecules and/or co-stimulatory molecules, and the signaling domain is derived from a primary signaling domain, such as the CD3 zeta domain. In embodiments, the signaling domain further includes one or more functional signaling domains derived from a co-stimulatory molecule. In embodiments, the co-stimulatory molecules are cell surface molecules (other than antigens receptors or their ligands) that are required for activating a cellular response to an antigen.

In embodiments, the co-stimulatory domain includes the intracellular domain of CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, or any combination thereof. In embodiments, the signaling domain includes a CD3 zeta domain derived from a T cell receptor.

The CAR molecules described herein also include a transmembrane domain. The incorporation of a transmembrane domain in the CAR molecules stabilizes the molecule. In embodiments, the transmembrane domain of the CAR molecules is the transmembrane domain of a CD28 or 4-1BB molecule.

Between the extracellular domain and the transmembrane domain of the CAR, there may be incorporated a spacer domain. As used herein, the term “spacer domain” generally means any oligo- or polypeptide that functions to link the transmembrane domain to the extracellular domain and/or the cytoplasmic domain on the polypeptide chain. A spacer domain may include up to 300 amino acids, preferably 10 to 100 amino acids, and most preferably 25 to 50 amino acids.

At present, in order to help expand CAR T cells in vivo, it is necessary to express antigen to stimulate the proliferation of CAR T cells, such as DC vaccine/lipid chain integrating antigen on the surface of DC/overexpression in certain immune cells Methods such as tumor cell surface antigens 3-5. This long-term amplification method that relies on TCR signals can stimulate the expansion of T cells in a large amount, but it will cause the cells to be exhausted and apoptosis very quickly, leaving the cells in a dysfunctional state. The expression of cytokines such as IL2/IL7/IL12/IL15/IL18/IL23/is one of the methods 6-9. Although IL12 and IL18 will rapidly expand cells, they will also lead to rapid cell differentiation and increase CAR—The exhaustion and toxicity of T cells, the expression of IL7/IL15 will keep the cells in the memory state, but it does not result in a good expansion of the cell number. At present, there is no way to maintain the cell memory state and rapidly expand.

We found the source genes of antigen-independent expansion through single-cell sequencing, which cannot be achieved by conventional methods such as overexpression factors. The present invention combines the downstream activation form molecules or persistent activation receptors of signals such as cytokine with solid tumor CAR to continuously express or induce the expression of persistent activation molecules in CAR to expand T cells. By inducing expression in CAR T to replace the role of cytokine, CAR T can be amplified in the state of naïve without or with little cytokine, enhancing its amplification effect and reducing side effects. After CAR T is amplified to a sufficient amount, the inducing factors are removed to further control its expansion. Also, the present invention expresses or knocks out transcription factors in solid tumor CAR. Allows CAR T to expand in the state of naïve without or with little cytokine, enhances its expansion effect and reduces side effects, and can reprogram T cells so that the depleted T cells can return to the state of naïve. In embodiments, by infecting T cells with multiple viruses, multiple gene expression composite T cells can be obtained from the T cell population, thereby achieving a stronger amplification effect.

The present disclosure describes compositions and methods for treating cancer. Embodiments relate to a cell modified to express one or more molecules at a level that is higher or lower than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, wherein the one or more molecules are identified in single-cell profiling analysis. Embodiments relate to a modified cell engineered to express an antigen binding molecule, wherein the expression and/or function of one or more molecules in the modified cell has been enhanced or reduced (including eliminated), where the one or more molecules are identified in single-cell profiling analysis. In embodiments, the modified cell comprises a disruption in an endogenous gene or addition of exogenous gene that is associated with a biosynthesis or transportation pathway of the one or more molecules. Embodiments relate to a pharmaceutical composition comprising the population of the cells.

Examples of overexpressed molecules include PLEKHN1, IL2, IL17F, IL31, IL3, CCL22, TNFSF4, PMCH, CCL1, XCL2, CCL17, TNIP3, IL5, G0S2, IL22, CSF2, CAVIN3, CCL4, CCL3, CCL4L2, IFNG, XCL1, CXCL10, ZBED2, CXCL9, CD40, FSCN1, GNLY, TPRG1, AL031777.3, LYN, LTA, CRTAM, GZMB, MIR155HG, MT2A, IL13, ELL2, RGS16, IER3, DUSP4, FABP5, LMNA, DUSP2, MYC, PHLDA2, BCL2A1, BCAT1, NPM3, CCDC50, HSP90AB1, ODC1, TXN, PIM3, RAN, NAMPT, H2AFZ, PRDX1, LGALS1, MIF, EIF4G2, CCL5, TAGLN2, TRAF1, TUBB, CDC42, TUBA1B, FTL, NFKBIA, PGAM1, PTMA, YWHAZ, TCP1, TPT1, CD70, PPIA, SEC61B, TMSB4X, PFN1, LDHA, HNRNPAB, BIRC3, NME2, TUBA1C, ATP5MC3, ANP32E, PTGES3, H3F3B, IL2RA, PKM, SH3BGRL3, HMGB1, ACTG1, ENO1, VIM, TMSB10, EIF1, SERBP1, TPM3, BTF3, CFL1, MYL6, ATP5MC2, ACTB, OAZ1, S100A4, and PGK1.

Embodiments relate to a method or use of polynucleotide, the method comprising providing a viral particle (e.g., AAV, lentivirus or their variants) comprising a vector genome, the vector genome comprising the polynucleotide encoding the one more molecules and a polynucleotide encoding an antigen binding molecule, the polynucleotide operably linked to an expression control element conferring transcription of the polynucleotides; and administering an amount of the viral particle to a subject such that the polynucleotide is expressed in the subject, where the one or more molecules are identified in single-cell profiling analysis. In embodiments, the AAV preparation may include AAV vector particles, empty capsids, and host cell impurities, thereby providing an AAV product substantially free of AAV empty capsids.

Embodiments relate to a method of causing or eliciting T cell response in a subject in need thereof and/or treating a tumor of the subject, the method comprising administering an effective amount of the composition of embodiment 6 to the subject. Embodiments relate to an isolated nucleic acid encoding one or more molecules associated with the metabolism of the modified cell.

In embodiments, the one more molecules comprise at least one of (overexpression or inducible overexpression) JAK2, STAT1, STAT2, STAT3, STAT4, PRKCA, PRKCQ, MAP3K1, MAP3K4, MAP3K8, MAPK14, BRAF, SMAD5, IL2RB, IL12RB2, IL18R1, IL21R, IL7R, CD28, Cavin3, ZBED2, MYC, EGFR, HER2, HER3, HER4, VEGFR2, VEGFR3, PDGFRα, PDGFRβ, gp130, IL-23R, IL-7R, CRLF2, βc, GHR, THPOR, EPOR, LepR, CSF3R, TNFR1, TGFBR1, TGFBR2, ACVR1A, BMPR2 ACVR1B, CXCR1, CXCR2, CXCR3, CXCR4, CCR2, and CCR5; and/or (knock out or knockdown) TOX, TOX2, TOX4, NR4A2, NR4A3, a functional variant of the one or more molecules, or a functional fragment of the one or more molecules.

In embodiments, the modified cell comprises an exogenous polynucleotide encoding modified STAT 1, STAT 2, and/or STAT 3. For example, one or more point mutations may be made such that the modified STAT 1, STAT 2, and/or STAT 3 can auto-phosphorylate to allow their signaling to be activated independently to enhance cell expansion and anti-apoptosis of the modified cell. In embodiments, the modified cell comprises at least one of SEQ ID NO: 35-43, 45-52, 54, and 55.

In embodiments, the cell modified to express one or more molecules at a level that is higher than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of JAK2, STAT1, STAT2, STAT3, STAT4, PRKCA, PRKCQ, MAP3K1, MAP3K4, MAP3K8, MAPK14, BRAF, SMAD5, IL2RB, IL12RB2, IL18R1, IL21R, IL7R, CD28.

In embodiments, the cell modified to express one or more molecules at a level that is higher than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of Cavin3, ZBED2, MYC.

In embodiments, the cell modified to express one or more molecules at a level that is higher than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of EGFR, HER2, HER3, HER4, VEGFR2, VEGFR3, PDGFRα, PDGFRβ, gp130, IL-23R, IL-7R, CRLF2, βc, GHR, THPOR, EPOR, LepR, CSF3R, TNFR1, TGFBR1, TGFBR2, ACVR1A, BMPR2 ACVR1B, CXCR1, CXCR2, CXCR3, CXCR4, CCR2, and CCR5.

In embodiments, the cell modified to express one or more molecules at a level that is lower than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of TOX, TOX2, TOX4, NR4A2, NR4A3.

In embodiments, the modified cell comprises an antigen binding molecule. In embodiments, the antigen binding molecule is the CAR, which comprises an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain. In embodiments, the antigen-binding domain binds to a tumor antigen is selected from a group consisting of: TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-11Ra, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGF-I receptor, CAIX, LMP2, gp100, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGSS, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRCSD, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51E2, TARP, WT1, NY-ESO-1, LACE-1a, MAGE-A1, legumain, HPV E6, E7, MAGE Al, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1, p53, p53 mutant, prostein, survivin and telomerase, PCTA-1/Galectin 8, MelanA/MART1, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG (TMPRSS2 ETS fusion gene), NA17, PAX3, Androgen receptor, Cyclin B1, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAXS, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRL5, and IGLL1. In embodiments, the intracellular signaling domain comprises a co-stimulatory signaling domain, or a primary signaling domain and a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, and NKG2D

In embodiments, the modified cell comprises the antigen binding molecule, the antigen binding molecule is a modified TCR (TCR) or TCR (TIL). In embodiments, the TCR is derived from spontaneously occurring tumor-specific T cells in patients. In embodiments, the TCR binds to a tumor antigen. In embodiments, the tumor antigen comprises CEA, gp100, MART-1, p53, MAGE-A3, or NY-ESO-1. In embodiments, the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains, or a combination thereof.

In embodiments, wherein the cell is an immune effector cell (e.g., a population of immune effector cells). In embodiments, the immune effector cell is a DC, macrophage, T cell, or NK cell. In embodiments, the immune effector cell is a T cell. In embodiments, the T cell is a CD4+ T cell, a CD8+ T cell, or a combination thereof. In embodiments, the cell is a human cell.

In embodiments, the enhanced expression and/or function of the one or more molecules is implemented by introducing a nucleic acid encoding the one or more molecules and/or the binding molecule, which is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector. In embodiments, the nucleic acid is an mRNA, which is not integrated into the genome of the modified cell. In embodiments, the nucleic acid is associated with an oxygen-sensitive polypeptide domain. In embodiments, the oxygen-sensitive polypeptide domain comprises HIF VHL binding domain. In embodiments, the nucleic acid is regulated by a promoter comprising a binding site for a transcription modulator that modulates the expression and/or secretion of the therapeutic agent in the cell. In embodiments, the transcription modulator is or includes Hif1a, NFAT, FOXP3, and/or NFkB.

Embodiments relate to a modified DC comprising a polynucleotide encoding an antigen binding molecule, which comprises an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain. Some embodiments relate to an isolated nucleic acid encoding an antigen binding molecule, which comprises an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain. Some embodiments relate to a pharmaceutical composition comprising the population of the cells. Some embodiments relate to a method of enhancing T cell response in a subject in need thereof and/or treating a tumor of the subject, the method comprising administering an effective amount of the composition to the subject. Some embodiments relate to a method or use of polynucleotide, the method comprising providing a viral particle (e.g., AAV, lentivirus or their variants) comprising a vector genome, the vector genome comprising the nucleic acid, the polynucleotide operably linked to an expression control element conferring transcription of the polynucleotides; and administering an amount of the viral particle to a subject such that the polynucleotide is expressed in the subject, where the one or more molecules are overexpressed in cancer cells, associated with recruitment of immune cells, and/or associated with autoimmunity. In embodiments, the AAV preparation may include AAV vector particles, empty capsids, and host cell impurities, thereby providing an AAV product substantially free of AAV empty capsids.

In embodiments, the expression of one or more molecules is regulated by one or more promoters. In embodiments, the polynucleotide comprises a promoter comprising a binding site for a transcription modulator that modulates the expression and/or secretion of the one or more molecules in the cell. For example, the transcription modulator is or includes Hif1a, NFAT, FOXP3, and/or NFkB. For example, the one or more molecules comprise at least one cytokine associated with an oxygen-sensitive polypeptide domain, and the oxygen-sensitive polypeptide domain comprises HIF VHL binding domain.

In embodiments, the polynucleotide may integrate into the genome of the modified cell, and descendants of the modified cell will also express the polynucleotide, resulting in a stably transfected modified cell. In embodiments, the modified cell may express the polynucleotide encoding the CAR, but the polynucleotide does not integrate into the genome of the modified cell such that the modified cell expresses the transiently transfected polynucleotide for a finite period of time (e.g., several days), after which the polynucleotide is lost through cell division or other factors. For example, the polynucleotide is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector, and/or the polynucleotide is an mRNA, which is not integrated into the genome of the modified cell.

At present, the most effective method for treating cancer is CAR T, but there are several problems in CAR T in solid tumors: 1. How to migrate into tumor cells; 2. Need DC cells to provide some special factors (such as IL12) 3. The ability to present new antigens by themselves. How to fully activate DC cells, before doing CAR-DC-like articles or CAR T CAR molecules, the activation of these two cells is very different (T cells mainly rely on TCR). The main signal of DC cells is derived from TOLL like Receptor). 2. The proportion of DC cells in peripheral blood is less than that of T cells, which is difficult to purify and culture. The present invention allows DC to specifically recognize tumors, enhance the function of DC cells, recruit other modified and unmodified immune cells through DC, and release various cytokines (IL12, etc.) through DC to promote immune system function through DC activation. Other immune cells, thereby enhancing the effectiveness of immunotherapy. Related experiments include: 1. nCAR-DC killing experiment, 2. tCAR-DC (TraditionCAR) killing experiment, 3. nCAR-DC+NT killing experiment, 4. tCAR-DC +NT killing experiment, 5. nCAR-DC+CAR-T killing experiment, 6.tCAR-DC+CAR T killing experiment. The present invention is based on a CAR designed by Toll-Like Receptor (TLR) to fully activate DC cells and to promote the function of DC cells to recognize tumors. At the same time, we can also express in DC cells with the structure of CAR suitable for CAR T, thereby activating DC cells and promoting the function of DC cells. It can also be a combination of CAR-DC and CAR T, TIL, TCR, and other cell therapies. The Signal domain includes 10 different TLRs; TLR1-10 (planned experiments using TLR9 or Myd88). Myd88: Myeloid differentiation factor, with the same TIR domain as the intracellular domain of the TLR molecule, is a key linker molecule in the TLR and plays a key role in transmitting downstream information. TRIF can produce IFN-[beta] and an adaptor protein containing a TIR domain.

In embodiments, the transmembrane domain comprises a transmembrane domain of at least one of the molecules listed in the following table (e.g., CD8 CD40).

Sequences of Molecules Transmembrane Domain CD8b SEQ ID NO: 1 CD8a SEQ ID NO: 2 CD40 SEQ ID NO: 3 CD4 SEQ ID NO: 4 CD5 SEQ ID NO: 5 CD3zeta SEQ ID NO: 6 CD22 SEQ ID NO: 7 CD28 SEQ ID NO: 8 CD33 SEQ ID NO: 9 CD64 SEQ ID NO: 10 CD80 SEQ ID NO: 11 CD86 SEQ ID NO: 12 CD134 SEQ ID NO: 13 CD137 SEQ ID NO: 14 CD154 SEQ ID NO: 15

In embodiments, the intracellular signaling domain comprises a signaling domain of at least one of TLR1, TLR2, TLR3, TLR4, TLRS, TLR6, TLR7, TLR8, TLR9, TLR10, TLR11, MYD88, TRIF, TRAM, and TIRAP. In embodiments, the intracellular signaling domain comprises a signaling domain of at least one of TLR9 and MYD88. In embodiments, the intracellular signaling domain comprises a signaling domain of at least one of the molecules listed in the following table.

Sequences of Molecules Signaling Domain TLR1 SEQ ID NO: 16 TLR2 SEQ ID NO: 17 TLR3 SEQ ID NO: 18 TLR4 SEQ ID NO: 19 TLR5 SEQ ID NO: 20 TLR6 SEQ ID NO: 21 TLR7 SEQ ID NO: 22 TLR8 SEQ ID NO: 23 TLR9 SEQ ID NO: 24 TLR10 SEQ ID NO: 25 MYD88 SEQ ID NO: 26 TRIF SEQ ID NO: 27 TRAM SEQ ID NO: 28 TIRAP SEQ ID NO: 29

In embodiments, the intracellular signaling domain comprises at least one of CD40 and RAGE

In embodiments, the antigen binding molecule is a CAR. In embodiments, the intracellular signaling domain comprises a co-stimulatory signaling domain, or a primary signaling domain and a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, and NKG2D

In embodiments, the the antigen-binding domain binds to a tumor antigen is selected from a group consisting of: TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-11Ra, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGF-I receptor, CAIX, LMP2, gp100, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGS5, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRC5D, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51E2, TARP, W1, NY-ESO-1, LAGE-1a, MAGE-A1, legumain, HPV E6, E7, MAGE Al, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1, p53, p53 mutant, prostein, survivin and telomerase, PCTA-1/Galectin 8, MelanA/MART1, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG (TMPRSS2 ETS fusion gene), NA17, PAX3, Androgen receptor, Cyclin B1, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAX5, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRLS, and IGLL1.

In embodiments, the antigen binding molecule further comprises a CD3 zeta domain. In embodiments, the antigen binding molecule is a modified TCR. In embodiments, the TCR is derived from spontaneously occurring tumor-specific T cells in patients. In embodiments, the TCR binds to a tumor antigen. In embodiments, the tumor antigen comprises CEA, gp100, MART-1, p53, MAGE-A3, or NY-ESO-1. In embodiments, the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains, or a combination thereof.

In embodiments, the cell is a human cell. In embodiments, the enhanced expression and/or function of the one or more molecules is implemented by introducing a nucleic acid encoding the one or more molecules and/or the binding molecule, which is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector. In embodiments, the nucleic acid is an mRNA, which is not integrated into the genome of the modified cell.

Embodiments relate to a cell modified to express one or more molecules at a level that is higher or lower than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, wherein the one or more molecules are identified in single-cell profiling analysis.

Embodiments relate to a modified cell engineered to express an antigen binding molecule, wherein the expression and/or function of one or more molecules in the modified cell has been enhanced or reduced (including eliminated), wherein the one or more molecules are identified in single-cell profiling analysis.

Embodiments relate to a method or use of polynucleotide, the method comprising providing a viral particle (e.g., AAV, lentivirus or their variants) comprising a vector genome, the vector genome comprising the polynucleotide encoding the one more molecules and a polynucleotide encoding an antigen binding molecule, the polynucleotide operably linked to an expression control element conferring transcription of the polynucleotides; and administering an amount of the viral particle to a subject such that the polynucleotide is expressed in the subject, where the one or more molecules are identified in single-cell profiling analysis.

Embodiments relate to a pharmaceutical composition comprising the population of the cells.

Embodiments relate to a method of causing or eliciting T cell response in a subject in need thereof and/or treating a tumor of the subject, the method comprising administering an effective amount of the composition to the subject.

Embodiments relate to an isolated nucleic acid encoding one or more molecules associated with the metabolism of the modified cell.

In embodiments, the modified cell comprises a disruption in an endogenous gene or addition of exogenous gene that is associated with a biosynthesis or transportation pathway of the one or more molecules.

In embodiments, the AAV preparation may include AAV vector particles, empty capsids, and host cell impurities, thereby providing an AAV product substantially free of AAV empty capsids.

In embodiments, the one more molecules comprise at least one of (overexpression or inducible overexpression) JAK2, STAT1, STAT2, STAT3, STAT4, PRKCA, PRKCQ, MAP3K1, MAP3K4, MAP3K8, MAPK14, BRAF, SMADS, IL2RB, IL12RB2, IL18R1, IL21R, IL7R, CD28, Cavin3, ZBED2, MYC, EGFR, HER2, HER3, HER4, VEGFR2, VEGFR3, PDGFRα, PDGFRβ, gp130, IL-23R, IL-7R, CRLF2, ⊖c, GHR, THPOR, EPOR, LepR, CSF3R, TNFR1, TGFBR1, TGFBR2, ACVR1A, BMPR2 ACVR1B, CXCR1, CXCR2, CXCR3, CXCR4, CCR2, and CCRS; and/or (knock out or knockdown) TOX, TOX2, TOX4, NR4A2, NR4A3, a functional variant of the one or more molecules, or a functional fragment of the one or more molecules.

In embodiments, the cell modified to express one or more molecules at a level that is higher than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of JAK2, STAT1, STAT2, STAT3, STAT4, PRKCA, PRKCQ, MAP3K1, MAP3K4, MAP3K8, MAPK14, BRAF, SMADS, IL2RB, IL12RB2, IL18R1, IL21R, IL7R, CD28.

In embodiments, the cell modified to express one or more molecules at a level that is higher than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of Cavin3, ZBED2, MYC.

In embodiments, the cell modified to express one or more molecules at a level that is higher than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of EGFR, HER2, HER3, HER4, VEGFR2, VEGFR3, PDGFRα, PDGFRβ, gp130, IL-23R, IL-7R, CRLF2, βc, GHR, THPOR, EPOR, LepR, CSF3R, TNFR1, TGFBR1, TGFBR2, ACVR1A, BMPR2 ACVR1B, CXCR1, CXCR2, CXCR3, CXCR4, CCR2, and CCR5.

In embodiments, the cell modified to express one or more molecules at a level that is lower than the level of the one or more expressed by a cell that has not been modified to express the one or more molecules, the one more molecules comprise at least one of TOX, TOX2, TOX4, NR4A2, NR4A3.

In embodiments, the modified cell comprises an antigen binding molecule.

In embodiments, the antigen binding molecule is the CAR, which comprises an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain.

In embodiments, the antigen-binding domain binds to a tumor antigen is selected from a group consisting of: TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-11Ra, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGF-I receptor, CAIX, LMP2, gp100, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGSS, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRCSD, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51 E2, TARP, WT1, NY-ESO-1, LAGE-1a, MAGE-A1, legumain, HPV E6, E7, MAGE A1, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1, p53, p53 mutant, prostein, survivin and telomerase, PCTA-1/Galectin 8, MelanA/MART1, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG (TMPRSS2 ETS fusion gene), NA17, PAX3, Androgen receptor, Cyclin B1, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAX5, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRLS, and IGLL1.

In embodiments, the intracellular signaling domain comprises a co-stimulatory signaling domain, or a primary signaling domain and a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, and NKG2D

In embodiments, the modified cell comprises the antigen binding molecule, the antigen binding molecule is a modified TCR (TCR) or TCR (TIL).

In embodiments, the TCR is derived from spontaneously occurring tumor-specific T cells in patients.

In embodiments, the TCR binds to a tumor antigen.

In embodiments, the tumor antigen comprises CEA, gp100, MART-1, p53, MACE-A3, or NY-ESO-1.

In embodiments, the TCR comprises TCRγ and TCRδ Chains or TCRa and TCR chains, or a combination thereof.

In embodiments, the cell is an immune effector cell (e.g., a population of immune effector cells).

In embodiments, the immune effector cell is a DC, macrophage, T cell, or NK cell.

In embodiments, the immune effector cell is a T cell.

In embodiments, the T cell is a CD4+ T cell, a CD8+ T cell, or a combination thereof.

In embodiments, the cell is a human cell.

In embodiments, the enhanced expression and/or function of the one or more molecules is implemented by introducing a nucleic acid encoding the one or more molecules and/or the binding molecule, which is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector.

In embodiments, the nucleic acid is an mRNA, which is not integrated into the genome of the modified cell.

In embodiments, the nucleic acid is associated with an oxygen-sensitive polypeptide domain.

In embodiments, the oxygen-sensitive polypeptide domain comprises HIF VHL binding domain.

In embodiments, the nucleic acid is regulated by a promoter comprising a binding site for a transcription modulator that modulates the expression and/or secretion of the therapeutic agent in the cell.

In embodiments, the transcription modulator is or includes Hif1a, NFAT, FOXP3, and/or NFkB.

Embodiments relate to a modified DC comprising a nucleic acid encoding an antigen binding molecule, which comprises an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain.

Embodiments relate to an isolated nucleic acid encoding an antigen binding molecule, which comprises an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain.

Embodiments relate to a method or use of polynucleotide, the method comprising providing a viral particle (e.g., AAV, lentivirus or their variants) comprising a vector genome, the vector genome comprising the nucleic acid, the polynucleotide operably linked to an expression control element conferring transcription of the polynucleotides; and administering an amount of the viral particle to a subject such that the polynucleotide is expressed in the subject, where the one or more molecules are overexpressed in cancer cells, associated with recruitment of immune cells, and/or associated with autoimmunity.

In embodiments, the AAV preparation may include AAV vector particles, empty capsids, and host cell impurities, thereby providing an AAV product substantially free of AAV empty capsids.

Embodiments relate to a pharmaceutical composition comprising the population of the cells.

Embodiments relate to a method of enhancing T cell response in a subject in need thereof and/or treating a tumor of the subject, the method comprising administering an effective amount of the composition to the subject.

In embodiments, the transmembrane domain comprises a transmembrane domain of CD8 or CD40.

In embodiments, the intracellular signaling domain comprises a signaling domain of at least one of TLR1, TLR2, TLR3, TLR4, TLRS, TLR6, TLR7, TLR8, TLR9, TLR10, TLR11, MYD88, TRIF, TRAM, and TIRAP.

In embodiments, the intracellular signaling domain comprises a signaling domain of at least one of TLR9 and MYD88.

In embodiments, the intracellular signaling domain comprises at least one of CD40 and RAGE

In embodiments, the antigen binding molecule is the CAR.

In embodiments, the intracellular signaling domain comprises a co-stimulatory signaling domain, or a primary signaling domain and a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, and NKG2D

In embodiments, the antigen-binding domain binds to a tumor antigen is selected from a group consisting of: TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-11Ra, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGF-I receptor, CAIX, LMP2, gp100, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGS5, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRC5D, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51 E2, TARP, WT1, NY-ESO-1, LAGE-1a, MAGE-A1, legumain, HPV E6, E7, MAGE Al, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1, p53, p53 mutant, prostein, survivin and telomerase, PCTA-1/Galectin 8, MelanA/MART1, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG (TMPRSS2 ETS fusion gene), NA17, PAX3, Androgen receptor, Cyclin B1, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAX5, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRLS, and IGLL1.

In embodiments, the antigen binding molecule further comprises a CD3 zeta domain.

In embodiments, the antigen binding molecule is a modified TCR.

In embodiments, the TCR is derived from spontaneously occurring tumor-specific T cells in patients.

In embodiments, the TCR binds to a tumor antigen.

In embodiments, the tumor antigen comprises CEA, gp100, MART-1, p53, MACE-A3, or NY-ESO-1.

In embodiments, the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains, or a combination thereof.

In embodiments, the cell is a human cell.

In embodiments, the enhanced expression and/or function of the one or more molecules is implemented by introducing a nucleic acid encoding the one or more molecules and/or the binding molecule, which is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector.

In embodiments, the nucleic acid is an mRNA, which is not integrated into the genome of the modified cell.

Embodiments relate to lymphocytes comprising one or more exogenous polynucleotides encoding MYC proto-oncogene, bHLH transcription factor (MYC), Caveolae Associated Protein 3 (CAVIN3) and/or Zinc finger bed-type containing 2 (ZBED2).

Embodiments relate to a method of enhancing an anti-tumor effect of a lymphocyte, the method comprising: introducing one or more exogenous polynucleotides encoding Caveolae Associated Protein 3 (CAVIN3) and/or Zinc finger bed-type containing 2 (ZBED2) into lymphocytes to obtain modified lymphocytes; contacting the modified lymphocytes with tumor cells that the modified lymphocytes bind; and allowing the modified lymphocytes to generate an anti-tumor effect, wherein the anti-tumor effect are enhanced as compared to those of lymphocytes without overexpressing CAVIN3 and ZBED2.

In embodiments, the exogenous polynucleotide comprises the amino acid of SEQ ID NO: 31, 32, and/or 33.

In embodiments, the lymphocytes are T cells or NK cells.

In embodiments, the anti-tumor effect is manifested by at least one of reduced cell exhaustion, enhanced cell expansion, and enhanced tumor growth inhibition.

In embodiments, a cell exhaustion level of the modified lymphocytes is lower than that of lymphocytes without overexpressing CAVIN3 and ZBED2.

In embodiments, a cell expansion level of the modified lymphocytes is higher than that of lymphocytes without overexpressing CAVIN3 and ZBED2.

In embodiments, tumor growth inhibition of the modified lymphocytes is greater than that of lymphocytes without overexpressing CAVIN3 and ZBED2.

In embodiments, a level of cytokine released by the modified lymphocytes is not significantly greater than that of lymphocytes without overexpressing CAVIN3 and ZBED2.

In embodiments, a level of activation of the modified lymphocytes is not significantly greater than that of lymphocytes without overexpressing CAVIN3 and ZBED2.

In embodiments, the lymphocytes comprise an antigen binding molecule.

In embodiments, the lymphocytes comprise a nucleic acid sequence encoding a dominant negative form of an inhibitory immune checkpoint molecule or a receptor thereof, and the inhibitory immune checkpoint molecule is selected from the group consisting of programmed death 1 (PD-1), cytotoxic T lymphocyte antigen-4 (CTLA-4), B- and T-lymphocyte attenuator (BTLA), T cell immunoglobulin mucin-3 (TIM-3), lymphocyte-activation protein 3 (LAG-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), leukocyte-associated immunoglobulin-like receptor 1 (LAIRI), natural killer cell receptor 2B4 (2B4), and CD 160.

In embodiments, the lymphocytes comprise a nucleic acid sequence encoding hTERT or a nucleic acid encoding SV40LT, or a combination thereof.

In embodiments, the lymphocytes comprise a nucleic acid sequence encoding a cytokine. In embodiments, the cytokine comprises IL-6, IL-7, IL-15, IL-12, or IFNγ.

In embodiments, the lymphocytes comprise a first population of T cells comprising a CAR binding a cell surface molecule of a white blood cell (WBC) and a second population of T cells comprising a CAR binding a solid tumor antigen.

EXAMPLES CoupledCAR®: T Cell Expansion Via CD19 CAR T and B Cells

FIG. 3 shows the expression of exhaustion markers on various cells. PAP CAR T cells, non-transferred T (NT) cells, and CD19 CART cells were co-cultured with B cells and/or substrate cells, respectively, and the expression of PD1 and Lag3 on these cells were measured (P-value<0.05=*, <0.01=**, <0.001=***, <0.0001=****; P≥0.05=no significance=NS). Flow cytometry analysis was used to measure exhaustion levels of the cells. The results showed that in a CoupledCAR® system, the CD19 CART cells killed the B cells and up-regulated PD1 and LAG3. These markers were not up-regulated in NT cells and PAP CAR T cells as compared to CD19 CAR T cells, indicating that the stimulation of PAP CAR T cells in the CoupledCAR® system did not rely on antigens and that expansion of PAP CAR T cells was with little exhaustion.

FIGS. 4-6 show the proportion of memory T cell, central memory T (Tcm) cell, and stem-like central memory T (Tscm) cell in various cells cultured as described for FIG. 3 (P-value <0.05=*, <0.01=**, <0.001=***, <0.0001=****; P≥0.05=no significance=NS). Flow cytometry analysis results showed that in the CoupledCAR® system, CD19 CART cells were differentiated into effector cells by killing B cells while few memory cells were observed. PAP CAR T cells and NT cells were not differentiated into effector cells and maintained a high proportion of memory cells and memory cells with stem cell phenotypes. Thus, the CoupledCAR® system helped PAP CAR T cells maintain high differentiation potential until contact with solid tumors.

FIG. 7 shows activation of B cells that are cultured with various cells (P value<0.05=*, <0.01=* *, <0.001=***, <0.0001=* * * *; P≥0.05=no significance=NS). Results of flow cytometry analysis showed that the expression of CD80 and CD86 are up-regulated on B cells. CD80 and CD86 are expressed as cell surface molecules by APCs (e.g., B cells) and are responsible for delivering signals to T cells. For example, along with CD80, CD86 provides co-stimulatory signals necessary for T-cell activation and survival. Thus, in the CoupledCAR® system, B cells are also activated, and these activated B cells interact with T cells by providing signals (e.g., co-stimulatory signals) to enhance T cell activation and/or expansion and survival.

These results show that, in the CoupledCAR® system, CD19 CAR up-regulated expression inhibition markers such as PD1 and LAG3 after activation of CAR-mediated TCR. But surprisingly, few of these inhibition markers were expressed on PAP CAR T and NT cells. Moreover, compared with CD19 CART cells, PAP CAR T and NT cells inhibited more phenotypes of Tscm and Tcm cells and fewer phenotypes of effector cells. Also, the CoupledCAR® system did not significantly reduce the number of memory cells of PAP CAR T and NT cells as compared to a non-coupled CAR system. In hematological malignancies, CAR T cells are directed against lineage antigens of B cells and encounter the antigens on normal and malignant B cells of the subject. These B cells act as antigen-presenting cells (APCs) that provide strong proliferation signals to expand CAR T cells and lead to the persistence of CAR T cells. These results demonstrate the role of B cells in the CoupledCAR® system and indicate that CAR T cells targeting other B cell antigen (e.g., BCMA, CD22, CD20, etc.) may replace CD19 CART cells in a CoupledCAR® system (CD19 CART and PAP CART cells) as shown in FIGS. 3-7.

In embodiments, compositions, methods, and sequences associated with CoupledCAR® system are described in PCT Publication Nos: WO2020106843 and WO2020146743, which are incorporated by reference in their entirety.

T Cell Expansion Via Bispecific Antibody and B Cells

On day 0, the peripheral blood of healthy volunteers was drawn, and CD3+ T cells were sorted with Pan T Kit. 100 ul of T cell Transact™ (for activating and expanding human T cells via CD3 and CD28) were added per 1×10⁷ T cells. On day 1, 4×10⁶ 1234 T cells were transduced with a lentivirus vector encoding CD19 CAR (Table 2), and the multiplicity of infection (MOI) was 10. 4×10⁶ 6503 T cells were transduced with lentivirus vectors encoding PAP CAR (Table 10), and the MOI was 49.98. 4×10⁶ T cells were non-transduced T cells (NT cells). On day 2, the media were changed to remove lentivirus vectors and T cell TransAct™.

TABLE 2 Name Construction Notes 1234 CAR-h19-bbz Humanized CD19 scFv and 4-1BB 6503 CAR-ACPP-bbz ACPP (or PAP) scFv and 4-1BB

FIG. 8 shows results of flow cytometry analysis of sorting of B cells and T cells. FIGS. 9 and 10 show results of flow cytometry analysis of expression of cell markers of co-cultured cells including B cells and T cells in the absence and presence of CD3-CD19 bispecific antibody (CD3-CD19 bispecific antibody), which was purchased from Biointron (catalog number of B302001). FIG. 11 shows flow cytokine results of cytokine release in the experiments of FIGS. 9 and 10. These results show CD3 positive T cells and CD19 positive B cells are connected via CD3-CD19 bispecific antibody, resulting in activation of T cells and cytokine release to lyse B cells.

FIG. 12 shows results of flow cytometry analysis of PAP CART cells co-cultured with B cells with or without the presence of CD3-CD19 bispecific antibody. PAP CAR T cells were generated and cultured for 7 days. B cells were isolated from PMBCs. CD3-CD19 bispecific antibody was mixed with PAP CAR T cells or PAP CAR T cells co-cultured with B cells. It was observed that after the 6503 cells mixed with CD3-CD19 bispecific antibody killed the B cells, 6503 cells appeared to be activated. FIG. 13 shows histograms of results of flow cytometry analysis of expression of various markers on T cells and B cells in the experiments of FIG. 12. PAP CAR T cells were further co-cultured with B cells for 24 hours, and flow cytometry was used to detect the cell membrane markers. It was observed that the 6503 cells co-cultured with or without B cells did not appear to be activated. However, when CD3-CD19 bispecific antibody was added to the media, 6503 cells co-cultured with B cells were activated. 6503 cells alone mixed with CD3-CD19 bispecific antibody showed some activation, which might be caused by T cell Transact™ used in the transduction of lentivirus vectors into T cells to generate 6503 cells. Thus, these results show that CD3-CD19 bispecific antibody can cause solid tumor CART cells (e.g., PAP CART cells) to be activated, as CD19 CART cells were in the previous Examples. The activation of PAP CAR T cells was indicated by the expression of CD69, CD25, and CD137 on CD4 and CD8 subtype T cells, which was significantly increased. Also, CD4OL expression of CD4 subtype T cells was up-regulated such as to allow these T cells to receive stimulation of CD40 positive APC cells. The amount of CD3-CD19 bispecific antibody is controllable; thus, these results indicate that CD3-CD19 bispecific antibody can cause the controllable activation of T cells by connecting and/or by narrowing the distance between T cells and B cells.

FIGS. 14 -16 show CellTrace™ analysis of the 6503 cells co-cultured with B cells in the presence or absence of CD3-CD19 bispecific antibody. 6503 cells alone or co-cultured with B cells were mixed with CD3-D19 bispecific antibody for 120 hours, and cell proliferation analysis was performed using CellTrace™. 1234 cells were used as a positive control. It was observed that neither the bispecific antibody nor the B cells alone could expand the T cells, while CD3-CD19 bispecific antibody caused the T cells co-cultured with B cell to be expanded.

FIG. 17 shows cytokine release results of CAR T cells co-cultured with B cells in the absence and presence of CD3-CD19 bispecific antibody. 6503 cells alone or co-cultured with B cells were mixed with CD3-CD19 bispecific antibody for 24 hours and then were analyzed using Cytometric Bead Array (CBA). 1234 cells were used as a positive control. It was observed that neither CD3-CD19 bispecific antibody alone nor B cells alone could make 6503 cells release cytokines, while 6503 cells co-cultured with B cells and CD3-CD19 bispecific antibody released cytokines. For example, the released cytokines included IL2 to promote activation and proliferation of T cells and IL6, TNF-α, and IFN-γ to provide an inflammatory environment. Thus, these results show that CD3-CD19 bispecific antibody can cause solid tumor CAR T cells (e.g., PAP CAR T cells) to be expanded, similar to the CD19 CAR T cells were in the previous Examples.

Further, CD19 CART cells and PAP CART cells were co-cultured with B cells for 24 or 48 hrs (hours), and single cell RNA (scRNA) profiling assay was performed on T cells, including both CD19 CART cells and PAP CAR T cells as well as B cells. FIG. 18 shows B cell clustering 24 hours after CD19 CART cells and PAP CART cells were co-cultured with these B cells. Two clusters of B cells were found in the 24 hrs samples: BC5 and BC7 clusters. Further analysis was performed to identify the phenotypes of the B cells. FIG. 19 shows the expression of surface markers of the B cells. It appears that the cells of BC5 and BC7 were in an activated state: BC5 differentiating towards BC7, and BC7 differentiating towards plasma cell, but not fully differentiated into plasma cells. FIG. 20 shows PAP CAR T cells clustering 24 and 48 hrs after CD19 CART cells and PAP CART cells were co-cultured with B cells. It appears that, as compared to 0 h, 24 hrs and 48 hrs showed enrichment of multiple CAR T cells, including Cluster 0 (C0) and Cluster 1 (C1). The expansion cluster in CD19 CAR T cells is C0; the expansion clusters in PAP CAR T cells are CO and Cl; and the expansion clusters in NT cells are C2, C4, and C10. C10 appeared to be similar to C0. It is speculated that C0 was differentiated from C10. Both groups of cells are CD4/CD8 double negative. The proliferation of CD19 CAR T cell groups has low interaction with B cells; PAP CAR T cells of Cl and NT cells of C2 appear to interact with B cells. FIG. 21 shows highly expressed genes in PAP CAR T cells in CB1. For example, CCR4 is highly expressed in Cl, and CCL17 and CCL22 bound to CCR4 were found to be highly expressed in B cells of C5. The interaction of the B cells and CAR T cells activates the JAK-STAT pathway, thereby inducing expansion of PAP CAR T cells, which is consistent with B cell ligand expression (CCL17 and CCL22) as shown in FIG. 21.

In sum, these results indicate several mechanisms involved in a CoupledCAR® system, which are shown in FIGS. 22-24. As shown in FIG. 22, B cells can be activated and become differentiated B cells, of which the expression of surface markers is shown in FIG. 19. The activation and differentiation of B cells can be implemented by various methods, for example, by using CD19 CART cells, CD19 antibody, bispecific antibody (e.g., CD3-CD19/BCMA), cytokines (e.g., IL4). T cells, including solid tumor CART cells, can also be activated to release cytokines to activate other APCs and DCs, and some B cells can be lysed, thereby releasing cell debris. These released cytokines and debris can activate APCs, including B cells and DCs. These APCs can upregulate co-stimulation molecules or ligands such as CD40, which can interact with T cells to cause or induce the expansion of T cells without corresponding binding antigens. Also, the interaction between differentiated B cells and T cells can cause or induce activation or expansion of T cells.

CoupledCAR®: Single-Cell RNA-Sequencing Analyses of Tumor Tissue from a Colorectal Cancer Patient with Thyroid Cancer after CAR T Cells Infusion

CAR T cell therapy in solid tumors is limited by various intrinsic and extrinsic factors, including poor expansion and a low degree of infiltration to the tumor site. The limitation of CAR T cell expansion against difficult-to-treat solid tumors has been recently addressed. To confirm CAR T cell infiltration into a solid tumor, deep single-cell RNA sequencing on T cells isolated from tumor tissue (lung metastasis) and on adjacent peripheral blood (PB) from a patient with thyroid cancer was performed. This study was also designed to depict the baseline landscape of infiltrating CAR T cells, especially the TSHR CAR T cells in thyroid cancer.

The T cells in this study included CAR-negative T cells (normal T cells) and CAR-positive T cells, which consisted of CD19 CART cells (CD19 CAR), TSHR CART cells (TSHR CAR), and T cells incorporated with both of the two CAR constructs (a CoupledCAR® system). These CAR-positive T cells in tumor tissue were predominantly TSHR CAR T cells and have shown a significant proportion of proliferative and cytotoxic T cells, which was evidenced by the signature gene expression.

Subsequently, a group of TSHR CART cell infiltration was observed. These cells also showed a high degree of cytotoxicity and trafficking activity, characterized by the high expression of known functional markers. Additionally, a large diversity of TSHR CAR T cell clones in tumor tissue was observed, which was different from TSHR CAR T cell clones in PB. The inferred developmental trajectory of CAR-positive CD8 T cells in PB and tumor tissue indicate that CAR T cell products described herein can undergo extensive transitions.

FIGS. 24A and 24B show that T cells derived from both PB and tumor tissue of a colorectal cancer patient with thyroid cancer are capable of robust proliferation and cytotoxicity. These data are restricted to T cells, including TSHR CAR, CD19 CAR, the CoupledCAR® system, and normal T cells. The integrated expression datasets derived from both peripheral blood (PB) and tumor tissue (lung metastasis) of the patient were applied to dimensional reduction analysis (t-SNE). Ten T cell clusters, including clusters of CD8 (proliferation, cytotoxicity, naïve, and effector memory), were identified. FIG. 24B. These clusters appear to be almost exclusively proliferative and cytotoxic T cells. There were 3447 proliferative T cells, and 77.7% of which were CAR-positive T Cells. There were 2431 cytotoxic T cells, and 82.8% were CAR-positive. These results show most of these CAR-positive T cells are cytotoxic and proliferative T cells, providing compelling evidence of the proliferative and antitumor capacity of the CAR T products described herein.

FIG. 25 shows that identification of all T cell clusters in PB and tumor tissue was evidenced by the expression of signature genes and known functional markers. These data are restricted to T cells, including TSHR CAR, CD19 CAR, the CoupledCAR® system, and normal T cells. Dynamic changes in gene expression between T cell clusters in peripheral blood (PB) and tumor tissue (lung metastasis) have been identified and were used for cluster analysis. It was observed that cytotoxic T cells in the C0 cluster were characterized by high expression of genes associated with cytotoxicity, including GNLY, GZMB, PRF1, CXCR3, and FGFBP2. Genes involved in the “cell cycle” and “proliferation” pathways, such as TYM, STMN1, MCM, HMGB1/2, and HMGN2, were highly expressed in corresponding clusters CD8-proliferation (C2, C4, C6). A well-defined subset of naïve T cells (C10) showed high expression of naïve markers (TCF7, CCR7, LEF1). Accordingly, the high expression of chemokines in the C12 cluster supported the potential migratory feature of these T cells.

FIGS. 26A-26C show that TSHR CAR T cells are significantly enriched in tumor tissue, confirming the capacity of CAR T cell infiltration into the tumor. These data are restricted to just TSHR CAR T cells. FIG. 26A. A total of 4670 single cells, including three subtypes, were isolated in the tumor tissue of the patient, among which pneumocytes accounted for 40.5%, monocytes for 14.5%, and T cells for 45.0%. FIG. 26B. CAR-positive T cells derived from tumor tissue appeared to be almost exclusively proliferative and cytotoxic T cells. FIG. 26C. The statistics of the TSHR CAR T cells in tumor tissue were compared with peripheral blood (PB) from the patient. TSHR CAR T cells in PB comprises 19.20% of T cells and 22.36% of CAR-positive T cells. Significant increases in levels of TSHR CAR T cells (38.38% of T cells and 70.60% of CAR-positive T cells) in tumor tissue, with an increase by a factor of 2-3 as compared with PB, was observed. CD19 CAR T cells were not enriched in tumor tissue (data not shown). These results show TSHR CART cells are significantly enriched in tumor tissue which confirms the capacity of CAR T cell infiltration into the tumor, and it is not surprising that tumor cells in the tumor tissue were not detected by deep single-cell RNA sequencing, given that the antitumor response against solid tumor-associated with cytotoxicity of the CART cells described herein.

FIGS. 27A-27D shows rare clonotype was found to be shared by TSHR CAR T cells in PB and tumor tissue. These data are restricted to just TSHR CAR T cells. FIG. 27A. 1055 and 501 TSHR CAR T cell clones in PB and tumor tissue, respectively, were identified. Only two clones with identical TCRs were detected. FIG. 27B. Only three clonotypes were present in at least two TSHR CAR T cells from PB. FIG. 27C. No clonotype was enriched in the TSHR CAR T cells from tumor tissue. FIG. 27D. One clonotype was found to be shared by TSHR CAR T cells in PB and tumor tissue. These results show one clonotype was found to be shared by TSHR CAR T cells in PB and tumor tissue, indicating diversity of TSHR CAR T cell clones between PB and tumor tissue.

FIGS. 28A-28D shows an inferred developmental trajectory of CAR-positive CD8 T cell in PB suggested a branched structure with differentiated proliferation and cytotoxicity T cells. These data are restricted to all CAR-positive CD8 T cells. FIG. 28A. The branched trajectory of CAR-positive CD8 T cell state in PB transited in a two-dimensional state-space with arrows showing the increasing directions of certain T cell properties. According to the original state labeled as the naïve T cells, differentiated T cells could be classified as proliferation and cytotoxicity, which undergo two distinct state transitions. FIGS. 28B, 28C, and 28D. Highly expressed signature genes exhibited distinct expression patterns among the corresponding three CD8 clusters: proliferative T cells with high expression of proliferation-related genes, naïve T cells with high expression of naive-related genes, cytotoxic T cells with high expression of cytotoxicity-related genes. These results show CAR-positive CD8 T cells in PB will be differentiated into two different fates: proliferation and cytotoxicity. Cell fate decisions are regulated by the high expression of signature genes.

FIGS. 29A-29D shows another inferred developmental trajectory of CAR-positive CD8 T cells in tumor tissue, suggesting a branched structure with differentiated proliferation and cytotoxicity T cells. These data are restricted to CAR-positive CD8 T cells. FIG. 29A. The branched trajectory of CAR-positive CD8 T cell state in tumor tissue transited in a two-dimensional state-space with arrows showing the increasing directions of certain T cell properties. According to the original state labeled as the naïve T cells, differentiated T cells could be classified as proliferation and cytotoxicity, which undergo two distinct state transitions. FIGS. 29B, 29C, and 29D. Highly expressed signature genes exhibited distinct expression patterns among our corresponding three CD8 clusters: proliferative T cells with high expression of proliferation-related genes, naïve T cells with high expression of naive-related genes, cytotoxic T cells with high expression of cytotoxicity-related genes. As well as T cells in PB, two subtypes of differentiated CAR-positive CD8 T cells with properties of proliferation and cytotoxicity were present in tumor tissue. The proliferative T cells appeared to exhibit high degrees of expansion in vivo, and cytotoxic T cells displayed profound antitumor activity.

FIG. 30 shows TSHR CAR T cells in tumor tissue exhibited a higher degree of trafficking and cytotoxicity, as compared with TSHR CAR T cells from PB. These data are restricted to just TSHR CAR T cells. Differential expression analyses of RNA-sequencing data of TSHR CAR T cells from PB and tumor tissue were performed and showed higher expression of trafficking-related and cytotoxicity-related genes in tumor tissue as compared to TSHR CAR T cells in PB. Cell cycle-related genes were being expressed at a higher level in PB. TSHR CAR T cells in tumor tissue exhibited a higher degree of trafficking and cytotoxicity, as compared with TSHR CAR T cells from PB.

Deep single-cell RNA sequencing was applied to a lung sample of the patient with thyroid cancer and characterized the T cell landscaping, especially the TSHR CAR T cells, which showed a significant proportion of proliferative and cytotoxic T cells in tumor tissue. Multiple comparisons between TSHR CAR T cells in PB and tumor tissue were performed and indicated that TSHR CAR T cells in tumor tissue had a higher capacity of cell infiltration, trafficking, and cytotoxicity as compared to TSHR CAR T cells in PB. These findings provide a plausible explanation for the positive responses of TSHR CAR T cells to immunotherapies for thyroid cancer. Additionally, CAR T cell products described herein might undergo extensive state transitions, which appeared to be shaped by two distinct processes, the CAR T cells proliferation, and tumor-induced CAR T cells cytotoxicity. Overall, this large compendium of single-cell data can elucidate the tumor-immune interactions by providing insights into the composition, states, and dynamics of CoupledCAR® T cell products in thyroid cancer. This approach for high-dimension and high-resolution characterization of single immune cells are applicable to other types of cancer and the use of other products for treating different types of cancer.

Based on the results from single-cell RNA profiling, multiple molecules were identified that appeared to enhance or weaken the performance of T cells (e.g., levels of T cell response), and the following molecules were selected from the multiple molecules for further investigation including overexpression based on previous studies and reports: JAK2, STAT1, STAT2, STAT3, STAT4, PRKCA, PRKCQ, MAP3K1, MAP3K4, MAP3K8, MAPK14, BRAF, SMAD5, IL2RB, IL12RB2, IL18R1, IL21R, IL7R, CD28, Cavin3, ZBED2, MYC, EGFR, HER2, HER3, HER4, VEGFR2, VEGFR3, PDGFRa, PDGFRβ, gp130, IL-23R, IL-7R, CRLF2, βc, GHR, THPOR, EPOR, LepR, CSF3R, TNFR1, TGFBR1, TGFBR2, ACVR1A, BMPR2 ACVR1B, CXCR1, CXCR2, CXCR3, CXCR4, CCR2, and CCR5; and/or (knock out or knockdown) TOX, TOX2, TOX4, NR4A2, and NR4A3. For example, further studies specified the performance of T cells with modulation of Cavin3, ZBED2, MYC, TOX, TOX2, TOX4, NR4A2, NR4A3.

CAR T Cell Co-Expressing MYD88 and Intracellular Domain of CD40

FIG. 31 shows a schematic diagram of vectors. FIG. 32 shows results of flow cytometry analysis of T cells expressing CAR, MYD88, and the intracellular domain of CD40. On day 0, Peripheral blood was extracted from healthy volunteers.CD3+ T cells were sorted by pan T Kit. 100 ul transActTM per 1×10⁷ T cells were added. On day 1, 4×10⁶ T cells were transfected with a 1234 vector (M01=10). 4×10⁶ T cells were transfected with 7408 vectors (MOI=34.65). On day 2, cultural media were changed. The lentivirus and TransAct™ were removed, and the cells were resuspended in fresh media (See Table 3). On day 7, flow detection of CAR expression was performed. Since both vectors are humanized antibodies, human CAR antibody detection is performed. The expression ratio of CAR T cells, including vector 1234, is 71.51%. The expression ratio of CART cells, including vector 7408, is 61.56%.

TABLE 3 K562 K562-CD19 B cell E:T systems 1234 − − − 60 × 10⁴:20 × 10⁴ Resuspend in 800 + − − ul texmacs − + − medium without − − + IL2 7408 − − − + − − − + − − − +

CAR T Cell Expressing CAVIN3 or ZBED2

FIGS. 34A and 34B (FIG. 34) show CAR expression and phenotypes of CAR T cells expressing CAVIN3 or ZBED2. T cells were transduced with lentivirus containing vectors CD19 CAR and CAVIN3 or ZBED2, and CAR expression and phenotypes of CAR T cells were analyzed. As shown in FIG. 34, overexpression of CAVIN3 and ZBED2 did not affect the expression of CAR, and the exhaustion levels of CD19 CAR T cells expressing CAVIN3 or ZBED2 were lower than CD19 CAR T cells that did not overexpress CAVIN3 and ZBED2. CAR T cells expressing ZBED2 showed more Naïve and memory-like phenotypes. In sum, CAVIN3 and ZBED2 did not affect the functions of CART cells, and CAVIN3 made CAR T cells differentiate towards effector T cells, while ZBED2 made cells differentiate to memory CAR T cells.

FIG. 35 shows cell activation of CAR T cells expressing CAVIN3 or ZBED2 after being co-cultured with substrate cells NALM6. NT or CD19 CAR T cells expressing CAVIN3 or ZBED2 were co-cultured with NALM6 cells at a ratio of 1:1. The CAR T cells showed normal activation, and the activation of CD19 CART cells that did not overexpress CAVIN3 and ZBED2 was higher than that of CD19 CART cells expressing CAVIN3 or ZBED2, indicating that expression of CAVIN3 or ZBED2 protected the cells from being over-activated.

FIG. 36 shows cell exhaustion of CAR T cells expressing CAVIN3 or ZBED2 after being co-cultured with substrate cells NALM6. NT or CD19 CAR T cells expressing CAVIN3 or ZBED2 were co-cultured with NALM6 cells at a ratio of 1:1. As shown in FIG. 36, cell exhaustion levels of CAR T cells expressing CAVIN3 or ZBED2 were lower than that of CAR T cells that did not overexpress CAVIN3 and ZBED2. Thus, the expression of CAVIN3 or ZBED2 helps reduce the exhaustion of CAR T cells, promoting the persistence of CAR T cells.

FIG. 37 shows cell phenotype changes of CAR T cells expressing CAVIN3 or ZBED2 after being co-cultured with substrate cells NALM6. NT or CD19 CART cells expressing CAVIN3 or ZBED2 were co-cultured with NALM6 cells at a ratio of 1:1. After co-culturing, while NT or CAR T cells differentiated towards effector cell phenotypes, CAR T cells CAVIN3 or ZBED2 maintained more cell phenotypes (less effector T cells like) than CAR T cells that did not overexpress CAVIN3 and ZBED2.

FIG. 38 shows cytokine release of CAR T cells expressing CAVIN3 or ZBED2 after being co-cultured with substrate cells NALM6. NT or CD19 CAR T cells expressing CAVIN3 or ZBED2 were co-cultured with NALM6 cells at a ratio of 1:1. After co-culturing, cytokines released by CAR T cells were measured. As shown in FIG. 38, these three types of CAR T cells showed similar cytokine release levels after being co-cultured with NALM6.

FIG. 39 shows tumor inhibition assay results of CART cells expressing CAVIN3 or ZBED2 after being co-cultured with substrate cells NALM6. NT or CD19 CART cells expressing CAVIN3 or ZBED2 were co-cultured with NALM6 cells at a ratio of 1:1. After co-culturing for various times, populations of tumor cells (NALM6) were analyzed. As shown in FIG. 39, tumor inhibition levels of CAR T cells CAVIN3 or ZBED2 were higher than that of CAR T cells that did not overexpress CAVIN3 and ZBED2.

FIG. 40 shows cell expansion of CAR T cells expressing CAVIN3 or ZBED2. NT or CD19 CAR T cells expressing CAVIN3 or ZBED2 were cultured with TEXMACS containing IL2 and counted on days 1, 5, 7, 10, 13, and 15. As shown in FIG. 39, cell expansion levels of CAR T cells CAVIN3 or ZBED2 were higher than that of CAR T cells without overexpressing CAVIN3 and ZBED2.

TABLE 4 Identifiers SEQ ID NO: CD8b SEQ ID NO: 1 CD8a SEQ ID NO: 2 CD40 SEQ ID NO: 3 CD4 SEQ ID NO: 4 CD5 SEQ ID NO: 5 CD3zeta SEQ ID NO: 6 CD22 SEQ ID NO: 7 CD28 SEQ ID NO: 8 CD33 SEQ ID NO: 9 CD64 SEQ ID NO: 10 CD80 SEQ ID NO: 11 CD86 SEQ ID NO: 12 CD134 SEQ ID NO: 13 CD137 SEQ ID NO: 14 CD154 SEQ ID NO: 15 TLR1 SEQ ID NO: 16 TLR2 SEQ ID NO: 17 TLR3 SEQ ID NO: 18 TLR4 SEQ ID NO: 19 TLR5 SEQ ID NO: 20 TLR6 SEQ ID NO: 21 TLR7 SEQ ID NO: 22 TLR8 SEQ ID NO: 23 TLR9 SEQ ID NO: 24 TLR10 SEQ ID NO: 25 MYD88 SEQ ID NO: 26 TRIF SEQ ID NO: 27 TRAM SEQ ID NO: 28 TIRAP SEQ ID NO: 29 Linker SEQ ID NO: 30 Cavin3 SEQ ID NO: 31 ZBED2 SEQ ID NO: 32 MYC SEQ ID NO: 33 STAT1wt SEQ ID NO: 34 STAT1 D165G SEQ ID NO: 35 STAT1 N179K SEQ ID NO: 36 STAT1 R274Q SEQ ID NO: 37 STAT1 R274W SEQ ID NO: 38 STAT1 K278E SEQ ID NO: 39 STAT1 Q285R SEQ ID NO: 40 STAT1 K298N SEQ ID NO: 41 STAT1 G384D SEQ ID NO: 42 STAT1 T385M SEQ ID NO: 43 STAT3 wt SEQ ID NO: 44 STAT3 N647I SEQ ID NO: 45 STAT3 G421R SEQ ID NO: 46 STAT3 Q344H SEQ ID NO: 47 STAT3 E415K SEQ ID NO: 48 STAT3 R152W SEQ ID NO: 49 STAT3 T716M SEQ ID NO: 50 STAT3 N420K SEQ ID NO: 51 STAT3 V353F SEQ ID NO: 52 STAT4 wt SEQ ID NO: 53 STAT4 Y693D SEQ ID NO: 54 STAT4 S721D SEQ ID NO: 55

All publications, patents, and patent applications cited in this specification are incorporated herein by reference in their entireties as if each individual publication, patent, or patent application were specifically and individually indicated to be incorporated by reference. While the foregoing has been described in terms of various embodiments, the skilled artisan will appreciate that various modifications, substitutions, omissions, and changes may be made without departing from the spirit thereof. 

1. A method of enhancing an anti-tumor effect of a lymphocyte, the method comprising: introducing an exogenous polynucleotide encoding Caveolae Associated Protein 3 (CAVIN3) or Zinc finger bed-type containing 2 (ZBED2) into lymphocytes to obtain modified lymphocytes; contacting the modified lymphocytes with tumor cells that the modified lymphocytes bind; and allowing the modified lymphocytes to generate an anti-tumor effect, wherein the anti-tumor effect of the modified lymphocytes is enhanced as compared to lymphocytes that do not express an exogenous CAVIN3 and ZBED2.
 2. The method of claim 1, wherein the lymphocytes are T cells or NK cells.
 3. The method of claim 2, wherein the anti-tumor effect comprises at least one of reduced cell exhaustion, enhanced cell expansion, and enhanced tumor growth inhibition.
 4. The method of claim 3, wherein the cell exhaustion level of the modified lymphocytes is lower than that of lymphocytes that do not express an exogenous CAVIN3 or ZBED2, the cell expansion level of the modified lymphocytes is higher than that of lymphocytes that do not express an exogenous CAVIN3 or ZBED2, and/or the tumor growth inhibition of the modified lymphocytes is greater than that of lymphocytes that do not express an exogenous CAVIN3 or ZBED2.
 5. The method of claim 1, wherein the exogenous polynucleotide encodes amino acid SEQ ID NO:
 31. 6. The method of claim 1, wherein the exogenous polynucleotide encodes amino acid SEQ ID NO:
 32. 7. The method of claim 1, wherein the lymphocytes comprises an antigen binding molecule.
 8. The method of claim 7, wherein the antigen binding molecule is a chimeric antigen receptor (CAR) comprising an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain.
 9. The method of claim 8, wherein the antigen-binding domain binds a tumor antigen comprising TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-11Ra, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGF-I receptor, CAIX, LMP2, gp100, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGSS, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRCSD, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51E2, TARP, \AM, NY-ESO-1, LACE-1a, MAGE-A1, legumain, HPV E6, E7, MAGE A1, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1 (Fra 1 or FosL1), p53, p53 mutant, prostein, survivin, telomerase, PCTA-1/Galectin 8, MelanA/MART1, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG, NA17, PAX3, Androgen receptor, Cyclin B1, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAX5, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRL5, or IGLL1.
 10. The method of claim 8, wherein the intracellular signaling domain comprises a co-stimulatory signaling domain, or a primary signaling domain and a co-stimulatory signaling domain, and wherein the co-stimulatory signaling domain comprises a functional signaling domain of a protein comprising CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, or NKG2D.
 11. The method of claim 7, wherein the antigen binding molecule is a modified T cell receptor (TCR) or tumor infiltrating lymphocyte (TIL).
 12. The method of claim 11, wherein the TCR is obtained from spontaneously occurring tumor-specific T cells in subjects.
 13. The method of claim 11, wherein the TCR binds a tumor antigen.
 14. The method of claim 13, wherein the tumor antigen comprises CEA, gp100, MART-1, p53, MAGE-A3, or NY-ESO-1.
 15. The method of claim 11, wherein the TCR comprises TCRγ and TCRδ chains, TCRα and TCR chains, or a combination thereof.
 16. The method of claim 1, wherein the lymphocytes comprise a nucleic acid encoding a dominant negative form of an inhibitory immune checkpoint molecule or a receptor thereof, and wherein the inhibitory immune checkpoint molecule comprises programmed death 1 (PD-1), cytotoxic T lymphocyte antigen-4 (CTLA-4), B- and T-lymphocyte attenuator (BTLA), T cell immunoglobulin mucin-3 (TIM-3), lymphocyte-activation protein 3 (LAG-3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), leukocyte-associated immunoglobulin-like receptor 1 (LAIRD, natural killer cell receptor 2B4 (2B4), or CD
 160. 17. The method of claim 1, wherein the lymphocytes comprise a nucleic acid encoding human telomerase reverse transcriptase (hTERT), a nucleic acid encoding SV40 large T antigen (SV40LT), or a combination thereof.
 18. The method of claim 1, wherein the lymphocytes comprise a nucleic acid encoding a cytokine.
 19. The method of claim 18, wherein the cytokine comprises IL-6, IL-7, IL-15, IL-12, or IFNγ.
 20. The method of claim 1, wherein the lymphocytes comprise a first population of T cells comprising a CAR binding a cell surface molecule of a white blood cell (WBC) and a second population of T cells comprising a CAR binding a solid tumor antigen. 